Contacts of the helix formed by residues 86 - 107 (chain B) in PDB entry 1T6S
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ARG 3.5 1.7 - - - +
82B GLN* 3.5 19.1 - - - +
83B LEU 3.8 5.4 - - - +
84B LEU 3.7 2.2 - - - -
85B ALA* 1.3 91.7 - - - +
87B VAL* 1.3 63.6 - - - +
88B ILE* 3.4 4.5 - - + +
89B GLN* 3.1 35.8 + - + +
90B ARG* 3.0 19.1 + - - -
413B NO3 3.0 21.8 - - - +
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TRP* 4.3 13.7 - - + -
81B ARG* 5.5 1.6 - - - +
85B ALA 3.7 1.0 + - - -
86B PRO* 1.3 69.7 - - - +
88B ILE* 1.3 64.8 + - + +
90B ARG* 3.1 29.4 + - - +
91B ARG* 2.9 42.9 + - - +
413B NO3 3.2 29.6 + - - +
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO* 3.4 4.3 - - + +
87B VAL* 1.3 81.2 - - + +
89B GLN* 1.3 61.7 + - - +
91B ARG* 3.3 34.4 + - + +
92B LEU* 3.1 36.7 + - + +
413B NO3 5.9 2.5 - - - +
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Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 3.4 23.2 - - + +
162A LEU* 3.6 19.9 - - + +
83B LEU 4.8 1.7 - - - +
84B LEU 3.0 20.1 + - - +
85B ALA* 3.8 2.0 - - - +
86B PRO* 3.1 34.6 + - + +
88B ILE* 1.3 78.8 - - - +
90B ARG* 1.3 57.5 + - - +
92B LEU* 3.3 9.7 + - - -
93B SER* 3.0 32.7 + - - -
401B NO3 2.8 32.2 + - - +
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 3.0 23.8 - - - +
105A TRP* 3.2 57.0 + - + +
107A GLN* 5.1 2.6 - - - +
81B ARG* 3.2 37.7 - - - +
85B ALA* 2.9 37.0 + - + +
86B PRO 3.0 9.4 + - - +
87B VAL* 3.1 38.2 + - - +
89B GLN* 1.3 78.1 - - - +
91B ARG* 1.3 52.3 + - - +
93B SER* 3.4 1.5 + - - -
94B ARG* 2.8 37.4 + - - +
401B NO3 3.7 8.7 - - - +
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Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TRP* 3.7 20.4 - - + -
87B VAL* 2.9 28.4 + - - +
88B ILE* 3.3 34.3 + - + +
90B ARG* 1.3 72.2 - - - +
92B LEU* 1.3 66.6 + - + +
94B ARG* 5.2 1.3 - - - +
95B SER* 3.0 26.0 + - - -
411B NO3 3.2 20.6 + - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 3.7 24.7 - - + +
88B ILE* 3.1 31.1 + - + +
89B GLN* 3.3 7.6 + - - +
91B ARG* 1.3 75.0 - - + +
93B SER* 1.3 63.9 + - - +
95B SER* 3.0 17.8 + - - +
96B MET* 3.0 19.6 + - + +
128B ARG* 4.5 27.1 - - - +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ALA* 4.0 8.7 - - - -
156A PHE* 3.5 11.7 - - - -
162A LEU* 3.3 25.3 - - - +
89B GLN 3.0 9.6 + - - -
90B ARG 3.7 2.7 - - - -
92B LEU* 1.3 77.1 - - - +
94B ARG* 1.3 64.1 + - - +
96B MET* 3.5 3.1 + - - +
97B LEU* 3.0 29.8 + - - +
401B NO3 2.7 38.7 + - - -
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Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA* 4.4 14.8 - - + +
104A ALA* 4.5 2.8 - - + +
105A TRP* 3.1 71.5 - - + +
90B ARG 2.8 21.8 + - - +
91B ARG* 5.2 2.0 - - - +
93B SER* 1.3 72.6 - - - +
95B SER* 1.3 60.4 + - - +
97B LEU* 3.2 6.1 + - - +
98B GLU* 2.8 54.4 + - + +
411B NO3 2.8 29.8 + - - +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG 3.0 10.8 + - - -
92B LEU* 3.0 9.2 + - - +
94B ARG* 1.3 75.6 - - - +
96B MET* 1.3 62.5 + - - +
98B GLU* 3.9 0.8 - - - +
99B VAL* 3.1 29.3 + - - +
118B ARG* 4.2 6.5 - - - +
123B ASP* 3.7 19.3 - - - -
125B SER* 3.7 2.7 - - - -
128B ARG* 2.7 24.6 + - - -
411B NO3 3.1 30.2 + - - -
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Residues in contact with MET 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A PHE* 3.3 35.4 - - + +
162A LEU* 5.2 7.2 - - + -
92B LEU* 3.0 13.0 + - - +
93B SER* 3.9 4.5 - - - +
95B SER* 1.3 81.8 + - - +
97B LEU* 1.3 59.1 + - - +
100B LEU* 3.0 30.5 + - - +
125B SER* 4.1 7.0 - - - +
128B ARG* 3.3 43.3 - - + +
129B LEU* 3.4 32.5 - - + +
132B ARG* 3.5 33.9 - - - +
134B LEU* 4.6 0.4 - - + -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.9 29.4 - - + +
100A LEU* 3.6 24.5 - - + +
101A ALA* 3.5 39.3 - - + +
104A ALA* 4.4 4.3 - - + -
156A PHE* 4.1 15.5 - - + -
160A PHE* 3.8 31.0 - - + -
93B SER 3.0 21.1 + - - +
94B ARG 3.6 3.4 - - - +
96B MET* 1.3 74.3 - - + +
98B GLU* 1.3 59.4 + - - +
100B LEU* 3.3 4.2 + - + +
101B ALA* 2.8 30.0 + - - +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA* 4.4 12.3 - - + +
94B ARG* 2.8 50.6 + - + +
95B SER 3.9 3.6 - - - +
97B LEU* 1.3 70.0 - - - +
99B VAL* 1.3 61.6 + - - +
101B ALA* 3.2 7.9 + - - +
102B VAL* 2.9 34.5 + - + +
118B ARG* 3.6 30.0 + - + +
411B NO3 3.7 4.6 + - - -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B SER 3.1 16.9 + - - +
96B MET 4.1 1.8 - - - +
98B GLU* 1.3 74.2 - - - +
100B LEU* 1.3 63.7 + - - +
102B VAL* 3.0 8.6 + - - +
103B VAL* 2.9 35.6 + - + +
114B ILE* 4.3 11.0 - - + -
118B ARG* 3.2 35.4 - - - +
123B ASP* 4.7 0.4 - - - +
125B SER* 3.5 19.1 - - - -
126B ILE* 3.9 26.7 - - + -
129B LEU* 3.8 15.3 - - + -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.6 20.2 - - + -
160A PHE* 4.1 24.2 - - + -
96B MET 3.0 16.3 + - - +
97B LEU* 3.4 6.3 - - + +
99B VAL* 1.3 77.0 - - - +
101B ALA* 1.3 57.1 + - - +
103B VAL* 3.4 3.1 + - - +
104B ALA* 2.9 27.2 + - - +
129B LEU* 3.8 20.1 - - + +
134B LEU* 4.2 14.8 - - + +
135B ILE* 4.1 14.8 - - + -
152B THR* 4.0 22.2 - - + -
156B PHE* 4.1 26.0 - - + -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ARG* 4.4 8.7 - - + +
97A LEU* 3.5 24.9 - - + +
98A GLU* 4.4 21.1 - - + +
97B LEU 2.8 18.4 + - - +
98B GLU* 3.4 9.9 - - - +
99B VAL 3.1 0.2 - - - -
100B LEU* 1.3 76.3 - - - +
102B VAL* 1.3 64.3 + - + +
104B ALA* 3.3 3.9 + - - +
105B TRP* 3.0 24.9 + - - +
417B NO3 4.1 3.1 + - - +
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 2.9 21.6 + - + +
99B VAL* 3.0 7.8 + - - +
101B ALA* 1.3 75.3 - - + +
103B VAL* 1.3 58.7 + - - +
105B TRP 3.3 0.3 + - - -
106B HIS* 2.8 47.1 + - + +
109B VAL* 5.1 0.4 - - + -
114B ILE* 4.1 24.2 - - + -
117B ILE* 4.0 24.7 - - + -
118B ARG* 3.9 24.7 - - + -
417B NO3 3.7 17.5 - - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 2.9 24.4 + - + +
100B LEU 3.7 6.3 - - - +
102B VAL* 1.3 73.4 - - - +
104B ALA* 1.3 65.3 + - - +
107B GLN* 2.9 29.8 + - - +
109B VAL* 4.1 8.3 - - + -
114B ILE* 4.0 25.6 - - + -
126B ILE* 6.0 0.2 - - + -
129B LEU* 5.3 0.2 - - + -
135B ILE* 4.1 23.1 - - + -
150B TYR* 3.8 15.0 - - + +
151B GLY* 3.6 37.5 - - - +
152B THR* 3.9 3.1 - - + +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 3.0 27.1 - - - +
93A SER* 4.0 16.6 - - - -
94A ARG 4.5 4.9 - - - +
97A LEU* 4.4 5.6 - - + -
408A NO3 3.4 17.7 - - - +
100B LEU 2.9 18.4 + - - +
101B ALA* 3.6 9.2 - - - +
103B VAL* 1.3 75.4 - - - +
105B TRP* 1.3 60.2 + - - +
107B GLN* 3.0 18.4 + - - +
152B THR* 3.9 6.5 - - + +
156B PHE* 5.1 0.2 - - + -
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Residues in contact with TRP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG* 4.7 1.6 + - - -
87A VAL* 4.2 11.9 - - + -
90A ARG* 3.2 69.7 + - + +
91A ARG* 3.7 30.3 - - + -
94A ARG* 3.1 53.9 - - + +
101B ALA 3.0 16.6 + - - +
104B ALA* 1.3 79.0 - - - +
106B HIS* 1.3 91.3 + + - +
107B GLN 3.6 0.4 + - - -
417B NO3 3.7 9.4 - - - +
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Residues in contact with HIS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG* 4.7 4.1 + - - +
102B VAL* 2.8 25.2 + - + +
105B TRP* 1.3 88.1 - + - +
107B GLN* 1.3 66.7 + - - +
108B PRO 3.4 10.6 - - - +
109B VAL* 3.8 17.9 - - + +
117B ILE* 3.7 34.1 - - + +
417B NO3 2.7 41.6 + - - -
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 3.4 20.1 + - - +
85A ALA* 3.5 19.6 - - + +
90A ARG* 5.1 1.3 - - - -
408A NO3 2.9 28.9 + - - -
103B VAL 2.9 15.5 + - - +
104B ALA* 3.0 24.9 + - - +
105B TRP 4.9 1.2 - - - +
106B HIS* 1.3 79.1 - - - +
108B PRO* 1.3 67.0 - - + +
109B VAL* 3.6 3.3 - - - +
138B ARG* 2.7 29.3 + - - -
150B TYR 3.5 15.3 - - - +
151B GLY* 3.2 2.4 - - - -
152B THR* 2.9 19.0 + - - -
422B NO3 3.6 5.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il