Contacts of the strand formed by residues 317 - 323 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS 3.4 2.7 + - - +
44A ASN* 3.0 45.8 + - + -
45A ILE 3.0 24.2 + - - -
46A ILE* 4.1 15.9 - - + -
141A LEU* 4.2 6.9 - - - +
142A ALA* 3.2 28.7 - - + +
307A ILE* 4.6 10.5 - - + -
310A LEU* 3.7 33.0 - - + +
311A SER* 3.8 19.7 - - - -
313A ASN 5.5 0.4 - - - -
316A GLY* 1.3 76.2 - - - +
318A PHE* 1.3 70.4 + - - +
319A LEU* 3.9 19.1 - - + -
355A PHE* 3.9 24.5 - + - -
446A LEU* 4.7 1.9 - - - +
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Residues in contact with PHE 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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45A ILE* 3.5 23.3 - - + +
47A LEU* 4.5 7.6 - - + -
132A ILE* 3.6 34.1 - - + -
133A LEU* 4.3 19.3 - - + -
136A ALA* 4.0 22.0 - - + -
141A LEU* 4.9 0.4 - - - +
142A ALA 3.1 6.0 + - - +
143A THR* 3.3 3.9 - - + -
144A GLY 2.9 26.4 + - - -
159A LEU* 4.2 12.1 - - + -
317A PHE* 1.3 76.4 - - - +
319A LEU* 1.3 63.7 + - - +
320A GLN* 4.1 35.7 - - + -
442A MET* 3.8 25.8 - - - -
446A LEU* 4.6 9.9 - - + -
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Residues in contact with LEU 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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45A ILE 2.9 8.7 + - - +
46A ILE* 3.3 13.6 - - + +
47A LEU* 2.8 26.3 + - - +
144A GLY* 3.4 24.0 - - - +
146A VAL* 3.9 17.3 - - + -
303A THR* 4.4 2.7 - - + +
306A ALA* 4.0 13.9 - - + -
307A ILE* 3.9 28.5 - - + -
310A LEU* 3.8 14.6 - - + -
317A PHE* 3.9 10.5 - - + -
318A PHE* 1.3 81.3 - - - +
320A GLN* 1.3 75.4 + - - +
321A VAL* 3.9 16.6 - - + -
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Residues in contact with GLN 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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47A LEU* 3.2 19.9 - - + +
49A ILE* 4.4 4.3 - - + -
109A TRP* 3.0 31.5 + - - -
144A GLY 3.0 7.6 + - - +
145A ASN* 3.7 5.1 + - - +
146A VAL* 2.8 33.5 + - - +
155A THR* 3.5 41.2 + - - +
156A PRO* 4.4 0.8 - - - +
159A LEU* 3.6 36.6 - - + +
318A PHE* 4.1 9.1 - - + -
319A LEU* 1.3 77.8 - - - +
321A VAL* 1.3 65.9 + - - +
322A GLU* 5.2 1.8 - - - +
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Residues in contact with VAL 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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46A ILE* 4.7 2.9 - - + -
47A LEU 2.7 9.2 + - - +
48A LEU* 3.1 27.6 - - + +
49A ILE* 2.7 32.4 + - - +
146A VAL* 3.4 11.0 - - + -
299A LEU* 3.4 35.4 - - + -
303A THR* 3.6 25.6 - - + +
319A LEU* 3.9 25.4 - - + -
320A GLN* 1.3 80.6 - - - +
322A GLU* 1.3 56.0 + - - +
345A LEU* 5.0 0.8 - - + +
348A ALA* 4.5 0.2 - - + -
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Residues in contact with GLU 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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49A ILE* 3.2 14.4 - - + +
51A ASP* 3.0 11.6 - - + +
146A VAL 2.9 12.9 + - - +
147A SER* 2.7 29.1 + - - +
148A THR* 3.3 22.7 + - - -
149A ALA* 4.2 0.9 - - - +
155A THR* 2.7 36.1 + - + +
156A PRO* 3.4 6.5 - - + +
299A LEU* 3.9 11.5 - - - +
320A GLN* 5.2 2.2 - - - +
321A VAL* 1.3 76.6 - - - +
323A GLY* 1.3 63.4 + - - +
324A ALA* 3.3 16.4 - - - +
452A MG 2.1 30.3 - - - -
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Residues in contact with GLY 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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49A ILE 2.8 12.4 + - - -
50A GLY* 3.9 1.1 - - - -
51A ASP 3.3 18.0 + - - -
148A THR* 4.1 4.3 - - - -
299A LEU* 3.9 16.8 - - - -
322A GLU* 1.3 70.5 - - - +
324A ALA* 1.3 62.9 + - - -
325A SER 3.5 2.5 + - - -
326A ILE* 3.9 15.6 + - - +
341A GLU* 5.3 4.0 - - - -
344A ASP* 5.4 1.1 - - - -
345A LEU* 4.1 14.4 - - - +
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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