Contacts of the strand formed by residues 302 - 308 (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 SER 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 4.2 0.2 - - - +
284A CYS 4.2 2.2 - - - -
286A PRO* 4.2 5.2 - - - +
301A GLY* 1.3 68.1 + - - -
303A GLU* 1.3 63.6 + - - +
321A TYR* 4.3 13.0 - - - -
322A ALA* 3.3 2.1 - - - +
323A GLU* 2.9 41.8 + - - +
328A LEU* 2.9 32.7 + - - +
331A SER* 3.1 34.9 + - - -
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Residues in contact with GLU 303 (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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32A ARG* 2.9 37.2 + - - -
266A THR* 2.7 30.2 + - - -
283A GLY* 3.6 1.9 - - - -
284A CYS* 2.8 40.1 + - + +
286A PRO* 3.7 12.9 - - + +
302A SER* 1.3 76.6 - - - +
304A VAL* 1.3 63.9 + - - +
305A LEU* 4.3 15.3 - - + -
319A VAL* 3.9 24.0 - - + +
321A TYR 3.3 11.0 - - - +
322A ALA* 4.3 8.8 - - + +
331A SER* 2.9 8.0 + - - -
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Residues in contact with VAL 304 (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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281A TRP* 4.0 17.9 - - + -
282A VAL 3.3 5.6 - - - +
283A GLY* 5.0 1.3 - - - -
303A GLU* 1.3 78.2 - - - +
305A LEU* 1.4 71.9 + - - +
319A VAL* 3.6 5.2 - - - +
320A VAL* 2.9 29.7 + - + -
321A TYR* 2.9 22.6 + - + +
331A SER* 5.2 0.2 - - - -
334A ALA* 3.5 35.4 - - + -
341A LEU* 4.4 5.4 - - + -
343A ILE* 3.8 34.5 - - + -
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Residues in contact with LEU 305 (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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264A PHE* 3.6 37.9 - - + -
266A THR* 4.1 8.1 - - + -
268A VAL* 4.7 3.6 - - + -
280A LEU 3.8 0.2 - - - +
281A TRP* 3.4 4.9 - - - -
282A VAL* 2.8 40.5 + - + +
284A CYS* 3.7 23.8 - - - -
303A GLU* 4.3 12.8 - - + -
304A VAL* 1.4 85.0 - - - +
306A ARG* 1.3 61.3 + - - +
307A ILE* 4.6 4.5 - - + -
317A VAL* 4.3 14.4 - - + -
318A THR 3.2 6.1 - - - +
319A VAL* 3.9 24.7 - - + -
320A VAL* 4.8 0.2 - - - -
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Residues in contact with ARG 306 (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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277A THR* 5.0 7.5 - - - +
279A ASP* 2.8 29.8 + - + +
280A LEU 3.3 6.1 - - - +
281A TRP* 3.6 38.4 - - + +
305A LEU* 1.3 74.0 - - - +
307A ILE* 1.3 63.2 + - - +
308A GLN* 3.5 39.3 + - + +
316A LYS 3.5 1.8 - - - +
317A VAL* 3.4 4.7 - - - +
318A THR* 2.9 36.4 + - - +
320A VAL* 3.7 20.6 - - + +
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Residues in contact with ILE 307 (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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245A ILE* 3.7 20.4 - - + -
262A LEU* 3.8 25.1 - - + -
264A PHE* 3.6 27.1 - - + -
279A ASP* 3.4 6.6 - - - +
280A LEU* 2.8 50.1 + - + +
282A VAL* 4.0 13.2 - - + -
305A LEU* 4.6 3.8 - - + -
306A ARG* 1.3 79.5 - - - +
308A GLN* 1.3 63.1 + - - +
310A ILE* 4.0 18.0 + - + +
315A PRO* 4.1 11.0 - - + -
316A LYS 3.3 5.2 - - - +
317A VAL* 4.3 14.1 - - + -
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Residues in contact with GLN 308 (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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279A ASP* 3.5 21.9 + - - +
306A ARG* 3.5 47.6 + - + +
307A ILE* 1.3 73.6 - - - +
309A ASP* 1.3 76.4 + - - +
310A ILE 3.3 3.3 + - - -
315A PRO* 3.5 2.8 - - - +
316A LYS* 2.8 54.4 + - + +
318A THR* 4.5 6.1 + - - -
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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