Contacts of the strand formed by residues 267 - 273 (chain A) in PDB entry 3SRG
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 LEU 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ARG 3.8 6.7 - - - +
28A PHE* 4.9 0.2 - - - -
29A ASN* 3.8 21.5 - - + -
240A LEU* 3.6 31.4 - - + +
241A LEU* 3.8 22.4 - - + -
243A HIS* 3.5 20.4 - - - +
266A THR* 1.3 70.1 + - - +
268A VAL* 1.3 62.1 + - - +
269A ASP 3.7 0.2 + - - -
284A CYS* 3.3 2.3 - - - -
285A HIS* 2.8 54.0 + - + +
288A GLY* 3.5 27.6 - - - +
291A ILE* 4.6 5.8 - - + -
292A PHE* 4.1 12.1 - - + -
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Residues in contact with VAL 268 (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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224A ASN* 4.3 0.3 - - - +
238A ALA* 3.8 15.1 - - + +
239A GLU 3.9 11.9 - - - +
240A LEU* 3.2 22.8 + - - +
244A LYS 3.3 33.4 - - - +
245A ILE* 4.1 7.0 - - + -
264A PHE* 4.0 25.6 - - + -
266A THR* 3.4 10.0 + - + +
267A LEU* 1.3 71.2 - - - +
269A ASP* 1.3 61.6 + - - +
282A VAL* 3.9 21.1 - - + -
283A GLY 4.1 3.1 - - - -
284A CYS* 4.0 11.7 - - - -
305A LEU* 4.7 1.8 - - + -
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Residues in contact with ASP 269 (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 GLU* 3.4 1.4 - - - +
224A ASN* 2.6 16.3 - - - +
225A GLY* 2.9 21.8 + - - -
238A ALA* 3.3 11.1 - - - +
268A VAL* 1.3 72.9 - - - +
270A ASN* 1.3 66.6 + - - +
282A VAL* 4.3 0.6 - - - +
283A GLY 2.9 18.1 + - - +
285A HIS* 2.7 36.0 + - + +
332A THR* 3.5 16.7 - - - +
1357A CA 2.4 30.3 - - - -
1358A OCH 2.7 22.4 + - - -
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Residues in contact with ASN 270 (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 GLU* 3.0 43.9 + - - -
54A ASP* 3.2 21.8 + - - +
168A ASN* 4.1 0.3 - - - +
169A ASP* 4.1 13.4 - - - +
224A ASN* 3.0 4.5 - - - +
225A GLY* 3.8 7.5 - - - -
269A ASP* 1.3 77.5 - - - +
271A ILE* 1.3 61.8 - - - +
281A TRP 3.8 0.7 - - - +
282A VAL* 3.4 6.9 - - - +
283A GLY 3.2 24.3 + - - -
332A THR 2.9 18.9 + - - +
333A VAL* 4.0 8.5 - - + +
1357A CA 2.2 25.8 - - - -
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Residues in contact with ILE 271 (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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169A ASP* 5.1 2.6 + - - +
225A GLY* 4.1 7.2 - - - +
226A ILE 4.1 5.4 - - - +
227A ASN* 2.8 41.9 + - + +
236A TYR* 3.7 28.3 - - + +
237A ILE 3.9 1.8 - - - -
238A ALA* 3.6 37.9 - - + +
245A ILE* 4.1 21.5 - - + -
270A ASN* 1.3 78.5 - - - +
272A SER* 1.3 68.7 + - - +
273A VAL* 4.2 1.1 - - + -
280A LEU* 3.8 25.4 - - + -
281A TRP 3.7 2.9 - - - +
282A VAL* 4.5 4.5 - - + +
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Residues in contact with SER 272 (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 LEU 4.6 5.0 + - - -
227A ASN* 3.6 4.5 - - - +
271A ILE* 1.3 76.9 + - - +
273A VAL* 1.3 64.8 + - - +
274A ASP 4.2 0.2 - - - -
280A LEU* 3.3 5.7 - - - -
281A TRP* 2.8 35.6 + - - -
333A VAL* 3.9 15.1 - - - +
334A ALA 3.0 30.0 + - - -
335A ALA* 3.9 16.0 - - - +
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Residues in contact with VAL 273 (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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227A ASN* 3.5 34.0 - - + +
228A ILE 3.6 21.5 - - - +
229A SER* 4.5 1.8 - - - -
230A PRO* 3.9 23.8 - - + -
236A TYR* 3.9 18.2 - - + -
271A ILE* 4.2 2.7 - - + -
272A SER* 1.3 82.1 - - - +
274A ASP* 1.3 70.0 + - - +
275A PRO* 3.4 9.6 - - + +
278A GLY* 4.0 10.8 - - - +
279A ASP 3.4 4.5 - - - +
280A LEU* 4.6 3.4 - - + -
281A TRP* 5.3 0.2 - - - -
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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