Contacts of the strand formed by residues 277 - 285 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102F LYS* 4.3 10.3 - - - -
103F LEU 3.4 7.2 - - - -
104F GLN* 4.7 1.5 + - - -
169F GLY* 3.6 2.9 - - - -
273F CYS* 2.9 29.4 - - - +
274F LYS 3.2 6.8 + - - -
275F GLY* 4.2 0.2 - - - -
276F GLU* 1.3 81.9 - - - +
278F LEU* 1.3 61.5 + - - -
279F TYR* 3.5 24.2 - - - -
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Residues in contact with LEU 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F ILE* 5.1 5.6 - - + -
101F ALA 3.8 0.7 - - - +
102F LYS* 3.4 2.9 - - - -
103F LEU* 2.7 57.4 + - + +
105F LEU* 4.3 7.9 - - + -
122F ALA* 5.2 2.0 - - + -
167F VAL* 3.7 13.9 - - + -
168F GLY 3.6 9.4 - - - +
273F CYS* 4.2 11.4 - - - -
276F GLU 4.3 0.2 + - - -
277F GLY* 1.3 73.7 - - - -
279F TYR* 1.3 65.4 + - - +
280F LEU* 3.2 24.9 + - + -
308F ILE* 4.0 20.6 - - + -
310F LEU* 3.2 33.7 - - + -
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Residues in contact with TYR 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F MET* 4.5 16.2 - - + -
101F ALA 3.7 3.4 - - - +
102F LYS* 3.6 32.7 + - + +
166F ALA 3.3 5.5 - - - +
167F VAL* 3.5 0.3 - - - -
168F GLY* 2.7 40.7 + - - +
169F GLY 3.9 1.6 - - - -
170F GLU* 3.3 35.2 - - - +
171F PRO* 3.3 41.2 - - + +
172F LEU 5.3 0.2 - - - +
237F THR* 5.8 0.2 - - + -
274F LYS* 4.5 5.7 + - + -
277F GLY* 3.5 25.1 - - - -
278F LEU* 1.3 76.4 - - - +
280F LEU* 1.3 64.8 + - - +
281F SER* 3.3 8.1 + - - +
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Residues in contact with LEU 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F ALA* 5.0 7.2 - - + -
53F LEU* 4.2 18.2 - - + -
100F MET* 3.2 4.3 - - - +
101F ALA* 2.9 34.7 + - + +
103F LEU* 4.0 26.2 - - + -
166F ALA 3.6 2.7 - - - -
167F VAL* 4.1 19.1 - - + -
278F LEU* 3.2 29.4 - - + -
279F TYR* 1.3 74.4 - - - +
281F SER* 1.3 64.7 + - - +
306F PHE* 3.5 40.6 - - + -
308F ILE* 4.0 11.0 - - + -
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Residues in contact with SER 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F LEU* 4.1 1.7 - - - +
98F TRP* 4.1 8.7 - - - -
99F SER 3.4 8.1 - - - -
100F MET* 4.0 0.9 - - - +
165F PHE* 2.9 3.2 - - - +
166F ALA* 2.7 41.6 + - - +
172F LEU* 4.4 14.5 + - - +
216F LEU* 4.0 25.0 - - - +
237F THR* 5.0 1.0 - - - +
279F TYR* 3.3 15.8 + - - +
280F LEU* 1.3 80.5 + - - +
282F CYS* 1.3 62.2 + - - +
306F PHE* 4.4 1.3 - - - -
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Residues in contact with CYS 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LEU* 3.6 25.1 - - + -
55F PRO* 6.2 2.5 - - - -
98F TRP* 3.6 7.4 - - - -
99F SER* 2.7 43.2 + - - +
164F VAL 3.0 15.3 - - - +
165F PHE* 3.4 12.3 - - + +
281F SER* 1.3 76.2 - - - +
283F VAL* 1.3 68.0 + - - +
284F ASP* 3.3 18.8 - - - -
304F ARG* 3.7 16.6 - - - +
306F PHE* 4.1 3.6 - - + -
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Residues in contact with VAL 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F THR 4.5 3.6 - - - +
98F TRP* 4.1 16.2 - - + -
99F SER* 4.8 4.3 - - - +
162F TYR* 3.4 17.7 - - + -
163F HIS* 2.7 19.2 - - - -
164F VAL* 2.7 36.3 + - + +
224F VAL* 3.2 34.5 - - + -
282F CYS* 1.3 83.1 - - - +
284F ASP* 1.3 77.2 + - - +
285F ILE* 3.8 10.1 - - + -
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Residues in contact with ASP 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F PRO* 5.3 5.3 - - - +
57F MET* 5.0 1.4 - - - +
129F VAL* 3.5 13.9 - - + +
162F TYR 3.3 0.4 - - - -
163F HIS* 2.9 29.5 + - + +
282F CYS* 3.3 13.3 - - - -
283F VAL* 1.3 90.1 - - - +
285F ILE* 1.3 66.6 + - - +
286F MET* 3.3 4.9 + - - +
301F GLY* 3.2 4.6 - - - -
302F LEU 3.1 42.2 + - - +
304F ARG* 2.6 42.2 + - - +
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Residues in contact with ILE 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F MET* 4.2 11.0 - - + -
96F PRO* 4.7 9.6 - - + -
160F SER 3.6 14.4 - - - +
161F GLN* 3.2 8.0 - - - +
162F TYR* 2.6 53.0 + - + +
163F HIS* 3.3 5.9 - - - -
224F VAL* 4.9 8.5 - - + -
283F VAL* 3.8 17.0 - - + -
284F ASP* 1.3 81.2 - - - +
286F MET* 1.3 62.8 + - - +
287F GLY* 3.6 13.2 - - - +
288F TRP* 4.9 2.9 - - + -
299F TRP* 3.8 33.0 - - + +
300F ARG 3.9 3.8 - - - -
301F GLY* 4.3 1.6 - - - -
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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
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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