Contacts of the strand formed by residues 317 - 323 (chain B) in PDB entry 2G9Y
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 PHE 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LYS 3.6 2.4 + - - +
44B ASN* 2.9 46.1 + - + -
45B ILE* 3.1 24.9 + - - +
46B ILE* 3.9 19.5 - - + -
141B LEU* 4.3 6.9 - - - +
142B ALA* 3.1 27.4 - - + +
307B ILE* 4.6 9.2 - - + -
310B LEU* 3.6 33.0 - - + +
311B SER* 3.8 19.3 - - - -
313B ASN 5.7 0.2 - - - -
316B GLY* 1.3 75.3 - - - +
318B PHE* 1.3 70.9 + - - +
319B LEU* 3.8 19.3 - - + -
355B PHE* 4.0 22.2 - + - -
446B LEU* 4.7 2.4 - - - +
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Residues in contact with PHE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 3.6 20.9 - - + +
47B LEU* 4.7 5.6 - - + -
132B ILE* 3.6 35.7 - - + -
133B LEU* 4.1 26.5 - - + -
136B ALA* 3.9 23.6 - - + -
141B LEU* 5.0 0.6 - - - +
142B ALA 2.8 7.6 + - - +
143B THR* 3.4 2.6 - - + -
144B GLY 2.8 28.6 + - - -
159B LEU* 4.1 22.4 - - + -
317B PHE* 1.3 75.5 - - - +
319B LEU* 1.3 66.7 + - - +
320B GLN* 4.0 26.5 - - + -
442B MET* 4.1 17.3 - - - -
446B LEU* 4.6 9.4 - - + -
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE 2.9 9.0 + - - +
46B ILE* 3.2 13.4 - - + +
47B LEU* 2.7 33.4 + - - +
144B GLY* 3.4 23.8 - - - +
146B VAL* 3.9 16.8 - - + -
303B THR* 4.4 2.9 - - + +
306B ALA* 4.0 22.0 - - + -
307B ILE* 4.0 22.7 - - + -
310B LEU* 4.0 6.3 - - + -
317B PHE* 3.8 17.5 - - + -
318B PHE* 1.3 80.3 - - - +
320B GLN* 1.3 68.5 + - - +
321B VAL* 3.9 17.7 - - + -
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Residues in contact with GLN 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 3.2 20.5 - - + +
49B ILE* 4.8 4.0 - - + -
109B TRP* 3.1 31.2 + - - -
144B GLY 3.1 7.2 + - - +
145B ASN* 3.8 6.3 + - - +
146B VAL* 2.8 28.9 + - - +
155B THR* 3.3 42.8 + - - +
156B PRO* 4.2 1.0 - - - +
159B LEU* 3.4 37.0 - - + +
318B PHE* 4.0 9.2 - - + -
319B LEU* 1.3 76.3 - - - +
321B VAL* 1.3 68.6 + - - +
322B GLU* 4.9 2.1 - - - +
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 4.6 3.8 - - + -
47B LEU 2.7 8.7 + - - -
48B LEU* 3.1 29.2 - - + +
49B ILE 2.8 24.8 + - - -
146B VAL* 3.4 11.2 - - + -
299B LEU* 3.5 27.4 - - + -
303B THR* 3.3 33.7 - - + +
319B LEU* 3.9 26.9 - - + -
320B GLN* 1.3 79.5 - - - +
322B GLU* 1.3 60.9 + - - +
323B GLY 4.2 0.2 + - - -
345B LEU* 4.8 1.4 - - + +
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 3.3 14.5 - - + +
51B ASP* 2.9 11.0 - - + +
146B VAL 2.8 16.6 + - - +
147B SER* 2.7 28.3 + - - -
148B THR* 3.4 18.4 + - - -
149B ALA* 4.4 1.0 - - - +
155B THR* 2.6 38.0 + - + +
156B PRO* 3.5 3.9 - - + +
299B LEU* 3.8 9.9 - - - +
320B GLN* 4.2 4.0 - - - +
321B VAL* 1.3 74.4 - - - +
323B GLY* 1.3 61.5 + - - +
324B ALA* 3.1 21.1 + - - +
452B MG 2.2 30.2 - - - -
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Residues in contact with GLY 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE 2.7 11.6 + - - -
50B GLY* 3.8 3.0 - - - -
51B ASP 3.1 21.1 + - - -
148B THR* 4.3 2.7 - - - -
299B LEU* 3.8 18.8 - - - -
322B GLU* 1.3 69.6 - - - +
324B ALA* 1.3 61.5 + - - -
325B SER 3.6 2.2 + - - -
326B ILE* 3.8 12.8 - - - +
341B GLU* 5.1 4.5 - - - -
344B ASP* 5.7 0.9 - - - -
345B LEU* 4.0 16.4 - - - +
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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