Contacts of the strand formed by residues 316 - 323 (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 LYS 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A ARG 3.5 1.7 - - - +
307A ILE* 3.3 3.8 - - - -
308A GLN* 2.8 65.7 + - + +
309A ASP* 4.9 5.1 - - + +
314A GLU 3.4 3.0 + - - +
315A PRO* 1.3 72.9 - - - +
317A VAL* 1.3 61.2 + - - +
318A THR* 4.5 9.0 - - - +
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Residues in contact with VAL 317 (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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262A LEU* 4.8 2.9 - - + -
264A PHE* 3.8 36.1 - - + -
305A LEU* 4.3 19.7 - - + -
306A ARG 3.4 7.6 - - - +
307A ILE* 4.3 15.3 - - + -
315A PRO* 3.6 14.2 + - + +
316A LYS* 1.3 77.3 - - - +
318A THR* 1.3 64.9 + - - +
319A VAL* 6.1 0.9 - - + -
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Residues in contact with THR 318 (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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305A LEU* 3.2 8.0 - - - -
306A ARG* 2.9 43.9 + - - -
308A GLN* 4.5 12.0 + - - -
316A LYS* 4.5 7.4 - - - +
317A VAL* 1.3 77.4 + - - +
319A VAL* 1.3 77.6 + - - +
320A VAL* 3.3 14.2 + - + +
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Residues in contact with VAL 319 (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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37A VAL* 3.6 26.9 - - + +
303A GLU* 3.9 19.1 - - + +
304A VAL 3.6 6.3 - - - +
305A LEU* 3.9 12.6 - - + -
317A VAL* 6.1 0.7 - - + -
318A THR* 1.3 80.7 - - - +
320A VAL* 1.3 62.1 + - - +
321A TYR 3.7 8.3 - - - +
322A ALA* 3.7 30.3 - - + -
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Residues in contact with VAL 320 (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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37A VAL* 3.6 11.6 - - - +
39A LEU* 3.6 26.5 - - + +
281A TRP* 3.7 35.9 - - + -
304A VAL* 2.9 14.8 + - + +
306A ARG* 3.7 23.6 - - + +
318A THR* 3.8 14.6 - - + +
319A VAL* 1.3 74.7 - - - +
321A TYR* 1.3 61.3 + - - +
341A LEU* 4.4 4.5 - - + -
355A LEU* 3.8 21.8 - - + -
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Residues in contact with TYR 321 (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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37A VAL* 3.4 17.5 - - - -
38A GLU* 4.9 2.2 - - - -
39A LEU* 3.9 32.1 - - + -
42A CYS* 4.2 10.7 - - - +
302A SER* 4.3 13.5 - - - -
303A GLU* 3.3 0.3 - - - -
304A VAL* 2.9 41.8 + - + +
319A VAL* 3.5 3.1 - - - +
320A VAL* 1.3 81.0 - - - +
322A ALA* 1.3 67.0 + - - +
323A GLU* 2.4 50.8 + - + +
327A VAL* 4.4 4.5 - - - +
328A LEU* 5.0 0.9 - - + -
341A LEU* 4.5 1.3 - - + -
343A ILE* 3.6 20.4 - - + -
351A LEU* 3.2 28.8 - - + +
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Residues in contact with ALA 322 (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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34A VAL* 3.8 11.7 - - + -
35A THR 3.7 18.2 - - - +
36A PRO* 3.4 4.9 - - - +
37A VAL* 2.9 33.5 + - - +
38A GLU* 5.8 0.3 - - - +
302A SER 3.3 8.7 - - - +
303A GLU* 4.3 9.2 - - + +
319A VAL* 3.7 19.7 - - + -
321A TYR* 1.3 81.5 - - - +
323A GLU* 1.4 66.2 + - - +
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Residues in contact with GLU 323 (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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34A VAL* 3.6 14.9 - - - +
36A PRO* 4.9 7.6 - - + -
301A GLY* 3.3 1.9 - - - -
302A SER* 2.9 36.8 + - - +
321A TYR* 2.4 39.0 + - + +
322A ALA* 1.4 75.8 - - - +
324A ASN* 1.3 60.4 + - - +
325A GLY 2.9 18.0 + - - +
326A THR* 3.1 3.7 + - - +
327A VAL* 2.8 32.3 + - - +
328A LEU* 2.9 29.8 + - - +
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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