Contacts of the strand formed by residues 80 - 94 (chain B) in PDB entry 1KY9
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 GLN 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B THR* 4.5 2.2 + - - +
37B VAL* 3.1 38.4 + - + +
38B ASN 3.8 1.6 - - - +
39B THR* 3.7 14.7 - - - +
40B PRO* 3.4 29.1 - - - +
79B GLY* 1.3 77.0 - - - +
81B GLN* 1.3 70.0 + - - +
82B GLN* 3.2 27.2 + - - +
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Residues in contact with GLN 81 (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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34B SER* 3.4 26.6 + - - +
35B THR* 3.0 17.5 - - - +
36B THR* 2.4 29.4 + - - +
80B GLN* 1.3 75.1 + - - +
82B GLN* 1.3 76.0 - - - +
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Residues in contact with GLN 82 (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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34B SER* 3.0 6.0 - - - -
35B THR* 2.7 41.2 + - + +
37B VAL* 3.0 37.9 - - + +
80B GLN* 3.2 27.7 + - - +
81B GLN* 1.3 94.0 - - - +
83B LYS* 1.3 68.3 + - - +
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Residues in contact with LYS 83 (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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32B GLU* 5.2 16.1 + - + +
33B GLY 3.3 10.3 - - - +
34B SER* 4.1 7.9 - - - -
82B GLN* 1.3 82.8 + - - +
84B PHE* 1.3 61.7 + - - +
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Residues in contact with PHE 84 (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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31B VAL* 4.5 7.0 - - + -
32B GLU* 3.7 3.5 - - - +
33B GLY* 2.8 62.0 + - - -
34B SER* 3.3 22.0 - - - -
35B THR* 4.0 16.2 - - + -
82B GLN 4.8 0.4 - - - +
83B LYS* 1.3 77.5 - - - +
85B MSE 1.3 78.2 + - - +
86B ALA* 4.2 19.3 - - + -
106B VAL 5.1 0.2 - - - -
108B ASP 3.9 15.7 - - - -
109B ASN* 3.7 20.0 - - + -
110B ALA 4.7 0.4 - - - -
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Residues in contact with MSE 85 (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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30B ASN* 6.0 5.4 - - - +
31B VAL 3.4 10.3 - - - +
32B GLU* 5.1 8.5 - - + +
84B PHE* 1.3 86.5 - - - +
86B ALA* 1.3 61.2 + - - +
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Residues in contact with ALA 86 (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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30B ASN* 3.6 3.8 + - - +
31B VAL* 2.8 36.5 + - + +
84B PHE* 4.2 12.5 - - + -
85B MSE 1.3 76.6 - - - +
87B LEU* 1.3 65.3 + - - +
105B HIS 5.2 2.0 - - - +
106B VAL* 3.6 30.5 - - + +
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Residues in contact with LEU 87 (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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29B ILE 3.1 11.9 - - - +
30B ASN* 4.1 17.5 - - - +
86B ALA* 1.3 80.7 - - - +
88B GLY* 1.3 60.2 + - - +
106B VAL* 3.8 9.3 - - - +
169B ASN* 3.8 35.7 - - - +
172B GLY* 3.8 26.7 - - - +
209B ASN* 5.5 12.3 + - - +
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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
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28B SER* 3.7 3.1 - - - -
29B ILE* 2.9 33.2 + - - +
87B LEU* 1.3 78.5 - - - +
89B SER* 1.3 64.5 + - - -
103B ASN* 6.0 0.2 - - - -
106B VAL* 3.7 19.8 - - - +
169B ASN* 4.8 10.6 - - - +
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Residues in contact with SER 89 (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* 4.6 6.3 - - - -
27B VAL 3.5 9.0 - - - -
29B ILE* 4.0 4.5 - - - -
88B GLY* 1.3 73.6 - - - -
90B GLY* 1.3 55.3 + - - +
102B THR* 2.6 28.8 + - - -
103B ASN* 4.4 8.5 + - - +
167B ILE 4.6 0.9 - - - -
168B GLY* 3.5 12.8 - - - -
169B ASN 3.4 21.1 + - - +
175B GLU* 3.2 21.7 + - - -
211B GLY* 4.9 4.0 + - - -
212B GLY* 4.5 17.7 - - - -
213B ALA 5.4 0.9 - - - -
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Residues in contact with GLY 90 (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* 3.6 5.2 - - - +
27B VAL* 3.0 30.6 + - - +
29B ILE* 4.0 4.3 - - - +
89B SER* 1.3 77.7 - - - +
91B VAL* 1.3 67.9 + - - +
100B VAL* 3.7 13.7 - - - -
101B VAL 3.0 13.7 - - - -
102B THR* 3.9 2.9 - - - -
212B GLY* 6.1 1.1 - - - -
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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
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25B SER* 3.6 7.4 - - - +
26B VAL* 4.5 9.2 - - + -
90B GLY* 1.3 79.3 - - - +
92B ILE* 1.3 66.1 + - - +
93B ILE* 3.3 6.6 + - + -
100B VAL* 3.2 5.5 - - - +
101B VAL* 2.8 51.0 + - + +
150B ILE* 3.3 41.1 - - + -
212B GLY 5.4 0.2 - - - -
213B ALA* 3.5 35.4 - - + +
221B LEU* 4.5 7.2 - - + -
224B ILE* 4.9 3.4 - - + -
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Residues in contact with ILE 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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24B PRO 3.9 11.0 - - - +
25B SER* 2.9 15.1 + - - +
27B VAL* 3.6 15.9 - - + -
90B GLY 4.3 0.2 - - - -
91B VAL* 1.3 70.0 - - - +
93B ILE* 1.3 65.1 + - - +
94B ASP 4.3 6.5 - - - +
95B ALA* 4.3 11.2 - - - -
98B GLY* 5.7 0.2 - - - -
99B TYR 3.5 7.0 - - - +
100B VAL* 3.9 10.8 - - + -
117B LEU* 3.7 29.6 - - + -
141B ILE* 4.6 2.5 - - + -
147B LEU* 3.8 19.7 - - + -
148B THR 3.0 35.0 - - - +
149B ALA* 3.6 10.5 - - + -
150B ILE 3.1 26.3 + - - -
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Residues in contact with ILE 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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91B VAL* 3.6 16.8 - - + +
92B ILE* 1.3 74.5 - - - +
94B ASP* 1.3 57.4 + - + +
99B TYR* 2.6 27.8 + - + +
101B VAL* 4.3 13.2 - - + +
138B LEU* 5.1 7.2 - - + -
149B ALA* 4.0 9.0 - - - +
150B ILE* 3.4 34.4 - - + +
152B MSE 3.1 39.2 - - + +
221B LEU* 3.9 12.1 - - + -
247B VAL* 6.0 1.6 - - + -
251B THR* 4.8 17.0 - - + +
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Residues in contact with ASP 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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92B ILE* 3.7 3.5 - - - +
93B ILE* 1.3 80.8 - - + +
95B ALA* 1.3 58.1 + - - +
96B ASP* 3.0 19.6 + - - +
97B LYS* 3.0 32.6 + - - +
98B GLY* 2.8 27.9 + - - -
99B TYR* 3.1 34.9 + - + +
149B ALA* 4.4 0.4 - - - -
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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