Contacts of the strand formed by residues 277 - 285 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LYS* 3.9 18.2 - - - -
103A LEU 3.3 9.0 - - - -
104A GLN* 3.9 4.4 + - - +
168A GLY 3.8 1.2 - - - +
273A CYS* 3.0 22.5 - - - +
275A GLY 2.3 24.1 + - - +
276A GLU* 1.3 69.1 - - - +
278A LEU* 1.3 61.1 + - - -
279A TYR* 3.6 18.1 - - - -
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 5.1 9.2 - - + -
101A ALA 3.7 0.3 - - - +
102A LYS* 3.3 5.4 - - - -
103A LEU* 2.9 47.8 + - + +
105A LEU* 3.6 21.1 - - + +
122A ALA* 5.3 5.4 - - + -
167A VAL* 3.7 13.9 - - + -
168A GLY 3.7 9.9 - - - +
271A PRO* 6.4 0.2 - - + -
273A CYS* 3.8 13.0 - - - -
277A GLY* 1.3 75.5 - - - -
279A TYR* 1.3 72.3 + - - +
280A LEU* 3.2 26.7 - - + -
308A ILE* 3.7 30.3 - - + -
310A LEU* 5.2 3.4 - - + -
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Residues in contact with TYR 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A MET* 4.3 14.8 - - + -
101A ALA 3.5 4.0 - - - +
102A LYS* 3.8 38.3 + - + +
167A VAL* 3.3 3.6 - - - -
168A GLY 2.8 39.8 + - - +
169A GLY 3.7 3.1 - - - -
170A GLU* 3.2 41.2 - - - +
171A PRO* 3.7 35.1 - - + +
172A LEU 5.1 1.3 - - - +
237A THR* 4.7 0.5 - - - +
274A LYS 4.8 4.9 + - - -
275A GLY* 5.2 1.4 + - - -
277A GLY* 3.6 20.4 - - - -
278A LEU* 1.3 73.2 - - - +
280A LEU* 1.3 66.9 + - - +
281A SER* 3.5 7.7 + - - +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 4.8 9.0 - - + -
53A LEU* 4.0 15.7 - - + -
100A MET* 3.4 1.6 - - - +
101A ALA* 2.9 32.3 + - + +
103A LEU* 3.7 23.1 - - + -
166A ALA 3.5 4.0 - - - -
167A VAL* 3.6 14.6 - - + -
278A LEU* 3.2 37.9 - - + -
279A TYR* 1.3 74.0 - - - +
281A SER* 1.3 66.1 + - - +
306A PHE* 3.5 42.4 - - + -
308A ILE* 3.8 13.2 - - + -
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Residues in contact with SER 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.1 2.8 - - - +
98A TRP* 4.2 5.6 - - - -
99A SER 3.4 7.6 - - - -
100A MET* 3.8 14.4 - - - +
165A PHE* 2.9 7.0 - - - +
166A ALA* 2.9 42.1 + - - +
172A LEU* 4.3 16.1 + - - +
216A LEU* 3.8 16.2 - - - -
237A THR* 5.2 0.9 - - - +
279A TYR* 3.5 8.8 + - - +
280A LEU* 1.3 79.4 - - - +
282A CYS* 1.3 61.8 + - - +
306A PHE* 4.6 1.3 - - - -
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Residues in contact with CYS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.0 28.5 - - - -
54A ASN 6.3 0.2 - - - -
55A PRO* 6.3 1.6 - - - -
98A TRP* 3.6 6.5 - - - -
99A SER* 2.9 31.8 + - - +
164A VAL 3.0 15.9 - - - +
165A PHE* 3.3 10.3 - - + +
281A SER* 1.3 76.8 - - - +
283A VAL* 1.3 76.1 + - - +
284A ASP* 3.6 13.5 - - - +
304A ARG* 3.8 20.9 - - - -
306A PHE* 4.4 1.3 - - + -
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A THR 4.3 4.5 - - - +
98A TRP* 3.9 25.4 - - + -
99A SER* 4.3 5.2 - - - +
162A TYR* 3.0 11.2 - - + +
163A HIS* 2.9 19.8 - - - -
164A VAL* 2.8 41.8 + - + -
224A VAL* 3.4 24.5 - - + -
282A CYS* 1.3 84.0 - - - +
284A ASP* 1.3 62.9 + - - +
285A ILE* 3.8 12.3 - - + -
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Residues in contact with ASP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PRO* 5.4 5.1 - - - +
57A MET* 5.0 2.3 - - - +
129A VAL* 3.6 14.5 - - + +
162A TYR 3.5 0.2 - - - -
163A HIS* 3.0 35.1 + - + +
282A CYS* 3.6 10.9 - - - -
283A VAL* 1.3 79.1 + - - +
285A ILE* 1.3 67.5 + - - +
286A MET* 3.5 5.5 - - - +
301A GLY* 3.3 6.2 - - - -
302A LEU 3.3 40.6 + - - +
304A ARG* 2.6 37.2 + - - +
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Residues in contact with ILE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A MET* 4.5 12.6 - - + -
96A PRO* 4.5 9.6 - - + -
160A SER 3.8 11.4 - - - +
161A GLN* 3.2 5.5 - - - +
162A TYR* 2.7 54.3 + - + +
163A HIS* 3.1 15.8 - - - -
224A VAL* 4.7 10.5 - - + -
283A VAL* 3.9 10.8 - - + +
284A ASP* 1.3 82.7 - - - +
286A MET* 1.3 64.1 + - - +
287A GLY 3.6 6.3 - - - +
299A TRP* 3.3 38.6 - - + +
300A ARG 3.7 4.7 - - - +
301A GLY* 4.6 1.1 - - - -
136E LEU* 4.9 8.1 - - + -
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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