Contacts of the helix formed by residues 92 - 111 (chain B) in PDB entry 3OTC
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 ARG 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 5.5 11.3 - - - +
13B GLU* 5.2 11.1 + - - +
14B ALA 4.5 12.3 + - - -
15B ASP* 3.7 22.0 + - - -
16B ASP* 2.7 37.7 + - - +
17B THR* 4.0 7.6 - - - +
89B PHE* 2.9 19.0 + - - +
90B LYS* 4.0 11.9 - - + +
91B ARG* 1.3 76.7 - - - +
93B ALA* 1.3 64.5 + - - +
94B SER* 3.2 18.9 + - - +
95B LYS* 3.2 33.8 + - + +
96B PHE* 3.3 15.0 + - - -
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Residues in contact with ALA 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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16B ASP* 2.9 30.4 + - + +
18B CYS* 3.9 19.5 - - - -
91B ARG 3.4 2.4 + - - -
92B ARG* 1.3 69.9 - - - +
94B SER* 1.3 64.0 + - - +
96B PHE* 3.0 17.7 + - - +
97B MET* 3.1 25.0 + - + +
131B VAL* 4.0 13.8 - - + +
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Residues in contact with SER 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET* 3.7 18.4 - - - -
129A GLY 4.0 11.1 + - - -
130A ARG* 4.6 9.9 - - - +
131A VAL 5.4 0.9 - - - -
16B ASP* 3.1 19.7 + - - -
92B ARG* 3.2 19.1 + - - -
93B ALA* 1.3 77.3 - - - +
95B LYS* 1.3 62.1 + - - +
97B MET* 3.3 13.5 - - - +
98B THR* 2.7 37.4 + - - +
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Residues in contact with LYS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP* 3.0 42.4 - - - +
129A GLY 4.8 2.0 - - - +
130A ARG* 5.0 9.9 - - + +
88B TRP* 4.1 2.5 - - + -
89B PHE* 3.3 60.8 + - + +
92B ARG* 3.2 30.1 + - + +
93B ALA 3.1 0.8 - - - -
94B SER* 1.3 80.1 + - - +
96B PHE* 1.3 65.2 + - - +
98B THR* 3.9 2.5 - - - -
99B HIS* 3.2 33.3 + - + +
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B CYS* 4.6 1.1 - - - -
24B VAL* 3.9 25.4 - - + -
26B VAL* 3.8 15.9 - - + +
82B PHE* 3.5 46.2 - + + -
86B THR* 4.1 21.8 - - + -
88B TRP* 3.6 31.4 - + + -
89B PHE* 5.0 2.0 - - + -
91B ARG* 3.6 31.9 - - - -
92B ARG 3.3 19.2 + - - -
93B ALA* 3.0 9.9 + - - +
95B LYS* 1.3 80.8 - - + +
97B MET* 1.3 59.7 + - - +
99B HIS* 4.6 0.3 - - - +
100B VAL* 3.0 31.5 + - - +
131B VAL* 4.3 4.0 - - + -
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Residues in contact with MET 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 5.8 0.7 - - - +
94A SER* 3.7 22.4 - - - -
97A MET* 2.9 39.0 - - + -
98A THR* 3.7 19.0 - - + +
16B ASP* 5.2 0.9 - - - +
26B VAL* 4.2 9.8 - - - +
93B ALA* 3.1 15.2 + - + +
94B SER* 3.3 27.1 - - - +
96B PHE* 1.3 77.5 - - - +
98B THR* 1.3 59.3 + - + +
100B VAL* 3.8 1.9 - - - +
101B ALA* 2.9 30.8 + - - +
130B ARG* 4.1 11.9 - - - +
131B VAL* 3.2 26.2 - - + -
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Residues in contact with THR 98 (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 MET* 3.8 27.8 - - + +
98A THR 4.7 0.7 - - - +
101A ALA* 4.0 16.0 - - + +
127A PHE 3.4 3.5 - - - +
128A ASP* 3.9 4.9 + - - -
129A GLY* 3.1 47.7 + - - +
94B SER 2.7 19.8 + - - +
95B LYS 3.7 2.6 + - - -
97B MET* 1.3 77.2 - - - +
99B HIS* 1.3 62.0 + - - +
101B ALA* 4.0 5.8 - - - +
102B SER* 2.8 33.3 + - - -
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Residues in contact with HIS 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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31A ARG* 3.3 50.3 - - + +
126A GLY* 5.2 1.2 - - - -
127A PHE 3.6 8.2 + - - -
128A ASP* 3.8 34.0 + - + +
65B LEU* 3.9 19.9 - - + +
88B TRP* 3.9 9.6 - + + -
89B PHE* 3.7 29.1 - + - -
95B LYS* 3.2 27.9 + - + +
98B THR* 1.3 79.9 + - - +
100B VAL* 1.3 63.5 + - - +
102B SER* 3.5 3.6 + - - -
103B GLN* 3.2 27.4 + - - +
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Residues in contact with VAL 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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26B VAL* 4.0 15.3 - - + -
28B LEU* 3.8 10.8 - - + -
61B VAL* 3.9 11.6 - - + +
65B LEU* 3.5 22.9 - - + -
80B PHE* 3.7 35.4 - - + -
82B PHE* 3.9 19.3 - - + -
96B PHE 3.0 20.8 + - - +
97B MET 3.5 2.8 + - - +
98B THR 3.2 0.2 - - - -
99B HIS* 1.3 79.4 - - - +
101B ALA* 1.3 64.1 + - - +
104B PHE* 3.0 26.9 + - - +
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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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98A THR* 4.1 29.8 - - + +
101A ALA* 4.9 0.7 - - + -
102A SER* 3.6 11.7 - - - +
28B LEU* 3.8 23.8 - - + -
97B MET 2.9 19.6 + - - +
98B THR* 4.0 4.3 - - - +
100B VAL* 1.3 77.1 - - - +
102B SER* 1.3 61.2 + - - +
104B PHE* 4.0 1.2 - - - +
105B ALA* 3.2 24.6 + - - +
127B PHE* 5.0 1.8 - - - +
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA* 3.7 20.6 - - - -
105A ALA* 3.3 19.0 - - - +
125A PRO 4.6 1.3 - - - -
127A PHE* 2.9 39.8 + - - -
98B THR 2.8 22.9 + - - -
99B HIS* 3.5 4.0 + - - -
101B ALA* 1.3 75.3 - - - +
103B GLN* 1.3 61.9 + - - +
105B ALA 3.3 0.5 + - - -
106B SER* 2.8 29.0 + - - -
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Residues in contact with GLN 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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31A ARG* 4.9 8.3 - - - +
124A PRO* 3.0 25.9 + - - +
125A PRO* 3.8 6.6 - - - +
126A GLY* 3.9 20.7 - - - +
60B THR* 3.9 14.3 - - + +
61B VAL* 4.0 26.9 - - + -
64B GLU* 3.8 32.9 + - + +
65B LEU* 5.2 4.8 - - + +
99B HIS 3.2 17.1 + - - +
100B VAL 4.0 1.6 - - - +
102B SER* 1.3 81.2 + - - +
104B PHE* 1.3 63.2 + - - +
106B SER* 3.5 0.3 + - - -
107B SER* 3.0 28.1 + - - -
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Residues in contact with PHE 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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28B LEU* 3.5 25.1 - - + -
54B MET* 3.5 52.5 - - + -
57B CYS* 3.4 27.5 - - + -
58B ALA* 3.4 23.1 - - + -
61B VAL* 3.7 10.7 - - + +
78B TYR* 4.3 9.2 - + + -
80B PHE* 4.0 7.2 - + - -
100B VAL 3.0 18.7 + - - +
101B ALA 4.0 2.2 - - - +
103B GLN* 1.3 78.6 - - - +
105B ALA* 1.3 57.3 + - - +
107B SER* 3.1 7.9 + - - -
108B TYR* 2.8 29.0 + + - +
127B PHE* 3.8 27.1 - + + -
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Residues in contact with ALA 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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102A SER* 3.3 34.8 - - - +
105A ALA* 4.2 0.2 - - + -
106A SER* 3.6 18.9 + - - +
101B ALA 3.2 17.4 + - - +
102B SER 3.7 3.4 - - - +
104B PHE* 1.3 80.7 - - - +
106B SER* 1.3 62.8 + - - +
108B TYR* 3.3 13.7 + - - +
109B VAL* 3.5 6.6 + - - +
127B PHE* 3.9 19.7 - - + -
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Residues in contact with SER 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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105A ALA* 3.6 19.3 + - - +
109A VAL* 3.6 14.5 - - - +
124A PRO* 3.6 15.7 - - - -
125A PRO* 2.7 40.4 + - - +
102B SER 2.8 13.9 + - - -
103B GLN* 3.6 4.9 - - - -
105B ALA* 1.3 77.9 - - - +
107B SER* 1.3 64.1 + - - +
109B VAL* 3.3 0.7 + - - -
110B PHE* 3.1 21.5 + - - +
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Residues in contact with SER 107 (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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124A PRO* 3.9 5.9 - - - +
57B CYS* 3.6 24.2 - - - -
60B THR* 3.0 33.6 + - - +
103B GLN 3.0 15.0 + - - -
104B PHE* 3.3 4.5 - - - -
106B SER* 1.3 81.3 - - - +
108B TYR* 1.3 56.4 + - - +
110B PHE* 4.1 6.7 - - - -
111B TYR* 2.9 43.3 + - - +
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Residues in contact with TYR 108 (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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33B PHE* 3.6 15.2 - + - -
36B PHE* 3.5 30.1 - + - -
42B PHE* 4.1 8.3 - - - -
50B ALA* 5.2 3.9 + - - +
53B LEU* 3.3 36.2 - - + +
54B MET* 3.9 25.6 - - + +
57B CYS* 3.3 17.9 - - - -
104B PHE* 2.8 12.9 + + - +
105B ALA* 3.5 14.8 - - - +
106B SER 3.2 0.2 - - - -
107B SER* 1.3 76.3 - - - +
109B VAL* 1.3 62.9 + - + +
112B TRP* 3.4 39.4 + + - +
116B PHE* 5.0 0.3 - - - -
121B LEU* 5.1 1.1 - - + -
125B PRO* 3.7 22.4 - - + -
127B PHE* 4.0 16.6 - + + -
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Residues in contact with VAL 109 (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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106A SER* 3.5 30.1 - - - +
109A VAL* 3.9 15.0 - - + +
110A PHE* 3.9 28.7 - - + +
105B ALA 3.7 12.6 - - - +
106B SER 3.3 2.7 + - - +
108B TYR* 1.3 74.5 - - - +
110B PHE* 1.3 68.1 + - - +
112B TRP* 3.4 13.9 + - - +
113B ARG* 5.0 0.7 + - - +
121B LEU* 3.6 30.0 - - + +
124B PRO* 4.7 2.2 - - + -
125B PRO* 4.4 9.9 - - + -
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Residues in contact with PHE 110 (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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109A VAL* 3.9 8.6 - - + +
121A LEU* 3.6 46.4 - - + -
122A LEU 3.6 21.5 - - - -
123A TYR* 3.9 2.7 - - - -
124A PRO* 3.8 27.8 - - + -
106B SER 3.1 17.3 + - - +
107B SER* 3.5 4.9 - - - +
109B VAL* 1.3 80.3 - - - +
111B TYR* 1.3 92.2 - + + +
112B TRP 3.3 2.3 + - - -
113B ARG* 4.4 7.3 + - - +
114B ASP* 5.5 0.7 - - - +
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Residues in contact with TYR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 4.4 10.1 - - + +
53B LEU* 3.8 13.5 - - + -
56B LYS* 3.9 38.7 - - + -
57B CYS 5.4 0.4 - - - -
60B THR* 3.5 25.0 + - - +
107B SER* 2.9 39.3 + - - +
110B PHE* 1.3 100.7 - + - +
112B TRP* 1.3 62.7 + - - +
113B ARG 3.3 2.7 - - - -
114B ASP* 3.1 40.1 + - - +
115B TYR* 3.5 10.9 - - + -
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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
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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