Contacts of the strand formed by residues 277 - 285 (chain B) in PDB entry 1SID
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 GLY 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B LYS* 4.1 15.9 - - - +
103B LEU 3.0 11.9 - - - -
104B GLN* 3.8 4.7 + - - +
168B GLY 4.1 0.2 - - - +
273B CYS* 2.8 25.5 - - - +
275B GLY 2.3 22.5 + - - +
276B GLU* 1.3 67.4 - - - +
278B LEU* 1.3 61.4 + - - -
279B TYR* 3.4 20.7 - - - -
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Residues in contact with LEU 278 (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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49B ILE* 4.9 6.7 - - + -
102B LYS* 3.1 4.5 - - - +
103B LEU* 2.7 56.5 + - + +
105B LEU* 4.3 6.3 - - + -
122B ALA* 5.1 3.1 - - + -
167B VAL* 4.2 15.5 - - + -
168B GLY 3.6 9.9 - - - +
271B PRO* 6.2 0.2 - - + -
273B CYS* 3.6 16.6 - - - -
276B GLU 4.3 0.2 + - - -
277B GLY* 1.3 75.0 - - - -
279B TYR* 1.3 74.2 + - - +
280B LEU* 4.0 16.8 - - + -
308B ILE* 3.9 35.7 - - + -
310B LEU* 4.0 13.7 - - + -
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Residues in contact with TYR 279 (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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100B MET* 4.4 11.2 - - + -
101B ALA 3.5 3.8 - - - +
102B LYS* 3.5 40.0 + - + +
166B ALA 3.7 0.5 - - - +
167B VAL* 3.3 3.1 - - - -
168B GLY 2.8 49.0 + - - +
169B GLY 3.8 2.0 - - - -
170B GLU* 3.2 30.9 - - - +
171B PRO* 3.5 38.2 - - + +
172B LEU 5.4 0.2 - - - +
237B THR* 5.6 0.9 - - + -
274B LYS 4.6 6.5 + - - -
275B GLY* 5.8 1.0 - - - -
277B GLY* 3.4 22.4 - - - -
278B LEU* 1.3 74.1 - - - +
280B LEU* 1.3 70.5 + - - +
281B SER* 3.9 6.5 + - - +
330F ASN* 5.9 0.2 + - - -
333F LEU* 4.4 15.1 - - - +
334F PRO 4.9 4.7 + - - -
336F VAL* 4.4 12.5 - - + +
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Residues in contact with LEU 280 (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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51B ALA* 4.9 7.6 - - + -
53B LEU* 3.6 24.5 - - + +
100B MET* 3.1 4.5 - - - +
101B ALA 2.9 35.1 + - - +
103B LEU* 4.1 25.8 - - + -
166B ALA 3.7 0.7 - - - -
167B VAL* 4.0 23.8 - - + -
278B LEU* 4.0 14.6 + - + -
279B TYR* 1.3 82.1 - - - +
281B SER* 1.3 63.6 + - - +
306B PHE* 3.6 38.6 - - + -
308B ILE* 4.0 12.8 - - + -
341F MET* 5.9 0.2 - - + -
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.9 1.3 - - - +
98B TRP* 3.8 8.5 - - - -
99B SER 3.5 6.7 - - - -
100B MET* 4.0 1.7 - - - +
165B PHE* 3.0 3.3 - - - +
166B ALA* 2.6 50.5 + - - +
172B LEU* 4.3 10.2 + - - +
216B LEU* 3.7 29.6 - - - +
237B THR* 5.0 1.9 - - - +
279B TYR* 3.9 8.5 + - - +
280B LEU* 1.3 80.7 + - - +
282B CYS* 1.3 63.4 + - - +
306B PHE* 4.7 0.5 - - - -
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Residues in contact with CYS 282 (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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53B LEU* 3.6 29.8 - - - -
54B ASN 6.5 0.2 - - - -
98B TRP* 3.4 9.4 - - - -
99B SER* 2.9 37.1 + - - +
164B VAL 2.9 14.8 - - - +
165B PHE* 3.2 12.1 - - + -
281B SER* 1.3 74.5 - - - +
283B VAL* 1.3 65.6 + - - +
284B ASP* 4.0 7.2 - - - -
304B ARG* 3.7 28.3 - - - +
306B PHE* 4.2 0.7 - - + -
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Residues in contact with VAL 283 (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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97B THR 4.4 3.1 - - - +
98B TRP* 4.0 23.3 - - + -
99B SER* 4.4 4.0 - - - +
162B TYR* 3.3 34.1 - - + -
163B HIS* 2.7 27.7 - - - -
164B VAL* 2.7 24.8 + - + +
224B VAL* 3.5 31.0 - - + -
282B CYS* 1.3 79.5 - - - +
284B ASP* 1.3 68.2 + - - +
285B ILE* 4.2 4.7 - - + -
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Residues in contact with ASP 284 (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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55B PRO* 5.5 4.2 - - - +
57B MET* 5.1 2.7 - - - -
129B VAL* 3.4 14.8 - - + +
162B TYR 3.2 2.2 - - - -
163B HIS* 2.8 28.1 + - + +
282B CYS* 4.0 3.5 - - - -
283B VAL* 1.3 88.1 + - - +
285B ILE* 1.3 67.5 + - - +
286B MET* 3.4 4.2 + - - +
301B GLY* 3.1 23.0 - - - -
302B LEU 3.3 23.6 + - - +
304B ARG* 2.7 45.8 + - - +
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Residues in contact with ILE 285 (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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136A LEU* 4.9 10.1 - - + -
57B MET* 3.7 20.2 - - + -
96B PRO* 5.0 6.3 - - + -
160B SER 3.4 13.0 - - - +
161B GLN* 3.0 21.2 - - - +
162B TYR* 2.6 48.0 + - + +
163B HIS* 3.3 7.3 - - - -
224B VAL* 5.0 7.2 - - + -
283B VAL* 4.2 8.3 - - + -
284B ASP* 1.3 80.7 - - - +
286B MET* 1.3 64.1 + - - +
287B GLY 3.3 14.1 - - - +
299B TRP* 3.4 28.9 - - + +
300B ARG 3.7 5.2 - - - +
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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