Contacts of the helix formed by residues 87 - 107 (chain B) in PDB entry 5SY1
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 LYS 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B HIS 4.5 4.8 + - - -
85B GLN 3.3 5.7 + - - +
86B HIS* 1.3 74.6 - - + +
88B GLY* 1.3 58.4 + - - +
89B LEU 3.5 1.3 - - - -
90B ALA* 4.4 3.8 - - - +
91B VAL* 3.3 27.6 + - + +
270B ARG* 3.9 29.5 - - - +
271B PHE* 4.5 20.1 + - - +
272B PRO 4.7 1.8 - - - -
273B LEU* 3.7 28.3 - - + +
276B ALA* 3.8 30.5 - - + -
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Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B HIS* 3.1 25.7 + - - -
87B LYS* 1.3 78.1 - - - +
89B LEU* 1.3 65.9 + - - +
91B VAL* 4.4 1.8 - - - +
92B ALA* 3.4 15.8 + - - +
195B PHE* 3.2 31.5 - - - -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 4.7 13.7 - - + -
86B HIS* 4.5 17.2 + - + +
87B LYS* 3.5 0.6 - - - +
88B GLY* 1.3 77.0 - - - +
90B ALA* 1.3 60.0 + - - +
92B ALA* 3.1 6.2 + - - +
93B VAL* 3.0 31.8 + - + +
138B LEU 5.0 0.2 - - - +
139B LEU* 4.0 11.4 - - + +
142B GLY* 4.0 24.9 - - - +
150B TYR* 6.1 0.2 - - + -
195B PHE* 5.2 0.4 - - - -
196B LEU* 4.9 7.0 - - + -
199B GLN* 3.8 29.4 - - + +
200B TYR* 3.7 36.6 - - + +
203B LEU* 5.2 9.2 - - + -
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 5.1 9.4 - - + -
80B PHE* 5.2 2.2 - - + -
86B HIS 5.4 1.0 + - - +
87B LYS* 4.4 4.0 + - - +
89B LEU* 1.3 75.7 - - - +
91B VAL* 1.3 65.6 + - - +
93B VAL* 4.3 0.2 - - - +
94B TYR* 3.1 38.2 + - + -
139B LEU* 3.8 18.2 - - + -
273B LEU* 4.2 23.3 - - + -
277B ILE* 4.1 19.7 - - + -
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 3.3 32.4 + - + +
88B GLY* 4.6 1.8 - - - +
89B LEU 3.4 0.4 - - - -
90B ALA* 1.3 76.2 - - + +
92B ALA* 1.3 63.3 + - - +
94B TYR* 4.4 0.7 - - - +
95B GLY* 3.1 19.6 + - - -
192B CYS* 4.6 1.6 - - - -
276B ALA* 4.4 6.3 - - + +
277B ILE* 3.9 32.5 - - + +
280B VAL* 3.8 40.6 - - + +
281B VAL* 5.2 1.8 - - + +
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLY 3.4 19.2 + - - +
89B LEU 3.1 6.1 + - - +
91B VAL* 1.3 79.4 - - - +
93B VAL* 1.3 62.9 + - - +
95B GLY 3.2 0.3 + - - -
96B VAL* 3.1 21.1 + - - +
192B CYS* 3.2 38.0 - - - +
195B PHE* 4.2 13.0 - - + -
196B LEU* 4.2 15.3 - - + -
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A TYR* 3.7 24.0 - - + +
89B LEU* 3.0 17.1 + - + +
90B ALA 3.5 1.1 + - - +
92B ALA* 1.3 73.4 - - - +
94B TYR* 1.3 60.6 + - - +
96B VAL* 3.1 8.1 + - - +
97B LEU* 2.9 31.9 + - + +
135B TYR* 4.4 19.1 - - + +
138B LEU* 4.4 17.0 - - + -
139B LEU* 3.7 31.4 - - + +
196B LEU* 4.5 17.0 - - + -
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Residues in contact with TYR 94 (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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493A SER 4.3 7.8 + - - -
494A TYR* 3.2 33.1 - + - -
497A PHE* 3.6 51.2 - + + -
80B PHE* 3.2 31.0 - + - -
90B ALA* 3.1 29.5 + - + +
91B VAL 4.4 0.4 - - - +
93B VAL* 1.3 76.5 - - - +
95B GLY* 1.3 58.1 + - - +
97B LEU* 3.9 5.5 - - + +
98B PHE* 3.0 30.5 + - - +
139B LEU* 5.0 4.7 - - + -
274B LYS* 5.2 4.3 - - + -
277B ILE* 3.7 43.1 - - + -
281B VAL* 4.0 9.4 - - + +
403B THR* 5.0 4.3 - - + -
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Residues in contact with GLY 95 (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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91B VAL 3.1 17.0 + - - -
92B ALA 3.6 5.4 - - - -
93B VAL 3.2 0.4 - - - -
94B TYR* 1.3 76.7 - - - +
96B VAL* 1.3 58.8 + - - +
98B PHE* 4.3 2.8 - - - +
99B CYS* 3.3 26.3 + - - -
188B PRO* 5.4 0.3 - - - +
189B GLN* 5.3 0.7 - - - -
192B CYS* 4.4 6.9 - - - +
280B VAL* 5.9 0.4 - - - -
281B VAL* 4.4 6.0 - - - +
284B ILE* 3.7 25.9 - - - +
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Residues in contact with VAL 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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92B ALA 3.4 15.0 - - - +
93B VAL* 3.1 10.4 + - - +
95B GLY* 1.3 77.7 - - - +
97B LEU* 1.3 64.9 + - - +
98B PHE 3.2 1.3 - - - -
99B CYS* 3.1 16.6 + - - +
100B LYS* 3.4 11.1 + - - +
135B TYR* 3.7 41.5 - - + +
189B GLN* 4.4 20.5 + - + +
192B CYS* 4.1 17.9 - - + +
193B LEU* 4.1 25.6 - - + +
196B LEU* 5.5 1.8 - - + -
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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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494A TYR* 3.4 39.3 - - + +
497A PHE* 4.3 17.7 - - + -
498A LEU* 3.6 23.0 - - + +
93B VAL* 2.9 24.0 + - + +
94B TYR* 4.0 8.1 - - + +
96B VAL* 1.3 76.9 - - - +
98B PHE* 1.3 61.2 + - - +
100B LYS* 3.9 5.2 + - - +
101B LEU 3.8 8.0 + - - -
131B TYR* 3.5 44.9 - - + +
132B PRO* 3.6 14.8 - - + -
135B TYR* 4.0 12.1 - - + -
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Residues in contact with PHE 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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497A PHE* 4.7 7.6 - + + -
498A LEU* 4.8 2.7 - - + -
501A VAL* 4.8 15.0 - - + -
94B TYR 3.0 18.0 + - - +
95B GLY* 4.7 4.3 - - - +
96B VAL 3.2 0.2 - - - -
97B LEU* 1.3 76.4 - - - +
99B CYS* 1.3 63.5 + - - +
101B LEU* 3.1 38.0 + - + +
102B VAL* 3.4 27.3 + - + +
281B VAL* 4.2 22.9 - - + -
284B ILE* 3.9 20.0 - - + -
285B ALA* 3.6 37.9 - - + -
288B GLN* 4.8 0.9 - - + -
407B ALA* 4.3 15.3 - - + -
411B CYS* 4.4 12.6 - - - -
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Residues in contact with CYS 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 GLY 3.3 19.3 - - - -
96B VAL 3.1 8.7 + - - +
98B PHE* 1.3 78.5 - - - +
100B LYS* 1.3 61.4 + - - +
102B VAL* 3.1 20.4 + - - +
103B GLY* 3.2 10.6 + - - -
185B GLY 5.7 3.8 - - - +
188B PRO* 4.1 20.0 - - - -
189B GLN* 4.1 30.2 - - + +
284B ILE* 3.9 22.0 - - - -
288B GLN* 4.9 7.2 - - - -
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Residues in contact with LYS 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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498A LEU* 5.8 0.7 - - + -
96B VAL 3.4 11.4 + - - +
97B LEU* 4.2 6.5 - - - +
98B PHE 3.3 0.8 - - - -
99B CYS* 1.3 78.3 - - - +
101B LEU* 1.3 62.5 + - - +
103B GLY* 3.8 2.3 + - - +
104B MET* 3.2 25.3 + - - +
131B TYR* 3.6 47.8 + - + +
135B TYR* 5.6 1.3 - - + -
189B GLN* 4.9 11.3 + - - +
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Residues in contact with LEU 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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498A LEU* 4.0 30.9 - - + +
501A VAL* 3.8 30.1 - - + -
502A MET* 4.8 13.5 - - + -
97B LEU 3.8 2.0 + - - -
98B PHE* 3.1 24.8 + - + +
100B LYS* 1.3 77.5 - - - +
102B VAL* 1.3 65.8 + - + +
104B MET* 3.3 22.2 + - + +
105B VAL* 3.4 23.3 + - + +
128B LEU* 3.8 29.2 - - + -
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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 PHE* 3.7 37.2 - - + +
99B CYS* 3.1 11.3 + - - +
101B LEU* 1.3 79.9 - - + +
103B GLY* 1.3 63.0 + - - +
104B MET 3.3 0.5 + - - -
105B VAL* 3.5 11.1 + - - +
106B LEU* 3.7 16.7 + - + +
181B TYR* 4.9 10.5 - - - +
288B GLN* 3.4 40.8 - - + +
292B LEU* 6.4 1.8 - - + -
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Residues in contact with GLY 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 CYS 3.2 10.3 + - - -
100B LYS* 3.8 2.7 + - - -
102B VAL* 1.3 80.5 - - - +
104B MET* 1.3 61.7 + - - +
105B VAL 3.3 0.2 - - - -
106B LEU* 3.5 9.8 + - - +
107B SER* 3.5 23.4 + - - -
110B PRO* 5.1 0.2 - - - +
176B GLN* 5.3 0.3 + - - -
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Residues in contact with MET 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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498A LEU* 6.5 0.9 - - - -
100B LYS 3.2 19.4 + - - +
101B LEU* 3.7 15.5 - - + +
102B VAL 3.2 1.4 - - - -
103B GLY* 1.3 76.4 - - - +
105B VAL* 1.3 65.4 + - + +
107B SER 2.9 20.4 - - - +
110B PRO* 4.0 22.2 - - + +
111B LEU* 5.8 1.6 - - + -
124B MET* 4.6 13.0 - - + +
127B ALA* 3.6 34.1 - - + +
128B LEU* 3.8 29.6 - - + -
131B TYR* 4.6 13.2 - - + +
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Residues in contact with VAL 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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502A MET* 5.8 7.0 - - + -
101B LEU* 3.4 24.6 + - + +
102B VAL* 4.0 7.6 - - - +
103B GLY 3.3 0.4 - - - -
104B MET* 1.3 82.6 - - + +
106B LEU* 1.3 70.6 + - + +
107B SER 3.9 2.9 - - - +
108B HIS* 5.1 6.2 + - - -
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Residues in contact with LEU 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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102B VAL* 3.7 21.5 - - + +
103B GLY* 3.5 9.8 + - - +
104B MET 3.3 0.6 - - - -
105B VAL* 1.3 86.3 - - + +
107B SER* 1.3 64.3 + - - +
108B HIS* 3.3 16.8 + - - -
176B GLN* 3.6 16.7 + - - +
177B ILE* 5.1 12.8 - - + -
181B TYR* 3.3 41.1 - - + +
292B LEU* 4.2 27.6 - - + -
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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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103B GLY 3.5 10.8 + - - -
104B MET 2.9 20.3 - - - +
105B VAL 3.9 1.6 - - - +
106B LEU* 1.3 76.4 - - - +
108B HIS* 1.3 62.1 + - - +
109B HIS* 2.8 37.0 + - - -
110B PRO* 3.3 18.7 - - - +
124B MET* 5.7 0.2 - - - +
176B GLN* 3.4 18.7 - - - +
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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