Contacts of the strand formed by residues 62 - 67 (chain A) in PDB entry 2PY2
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 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A PHE* 3.4 21.5 - - - -
55A THR* 4.1 1.5 - - - +
60A ILE 2.8 21.5 + - - -
61A PRO* 1.3 73.8 + - - +
63A TRP* 1.3 61.9 + - - +
103A GLN* 3.4 6.6 - - - +
104A MET* 2.7 45.8 + - - +
121A HIS* 4.6 0.9 - - - -
122A SER* 3.3 12.8 - - - -
123A SER* 4.0 1.3 - - - -
124A ILE* 4.0 25.0 - - - +
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Residues in contact with TRP 63 (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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23A LEU 3.1 27.6 + - - -
24A HIS 4.2 0.2 - - - -
25A TRP* 3.4 33.2 - + + +
28A ALA* 4.2 5.8 - - + -
39A LEU* 4.1 7.1 - - + +
62A SER* 1.3 72.3 - - - +
64A ILE* 1.3 62.3 + - - +
101A CYS* 3.5 35.0 - - + -
102A ILE 3.4 20.2 - - - -
103A GLN* 4.1 7.4 - - + -
115A THR* 3.3 23.8 - - - -
116A PRO 3.3 16.4 - - - -
117A CYS* 3.8 7.9 - - - -
119A HIS* 3.2 21.2 + - + -
121A HIS* 3.7 33.2 - + + +
122A SER 2.9 10.4 + - - +
123A SER* 3.7 8.3 - - - -
124A ILE* 3.2 25.1 + - - +
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Residues in contact with ILE 64 (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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25A TRP* 3.0 20.1 + - - -
39A LEU* 3.7 7.4 - - - -
40A ALA* 3.5 13.2 - - + +
42A ILE* 4.3 11.0 - - + -
63A TRP* 1.3 79.1 - - - +
65A GLY* 1.3 60.0 + - - +
66A GLY 3.1 4.8 + - - -
77A TRP* 3.9 17.0 - - + -
102A ILE* 3.1 45.9 + - + +
104A MET* 3.7 33.4 - - + -
112A TRP* 3.8 27.6 - - + +
124A ILE* 4.1 11.7 - - + -
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Residues in contact with GLY 65 (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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25A TRP* 4.2 9.6 - - - -
39A LEU* 3.3 30.1 - - - +
40A ALA 2.9 16.6 + - - -
64A ILE* 1.3 70.3 - - - +
66A GLY* 1.3 56.3 + - - +
67A THR* 4.8 0.3 - - - +
76A PHE 3.7 0.7 - - - +
77A TRP* 3.3 7.8 - - - -
78A MET* 2.9 35.1 + - - +
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Residues in contact with GLY 66 (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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25A TRP* 4.3 0.2 + - - -
64A ILE 3.1 6.0 + - - +
65A GLY* 1.3 77.4 - - - +
67A THR* 1.3 68.3 + - - +
76A PHE 3.2 9.0 - - - -
77A TRP* 3.4 19.2 - - - -
83A MET* 4.2 1.1 - - - -
102A ILE* 2.9 40.4 + - - +
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Residues in contact with THR 67 (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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25A TRP* 3.6 35.9 - - + -
65A GLY 4.8 0.7 - - - +
66A GLY* 1.3 81.5 - - - +
68A ASP* 1.3 60.1 + - - +
69A CYS* 3.4 21.3 + - - +
70A GLN* 4.3 10.0 + - - +
74A ARG 3.8 0.5 - - - +
75A TRP* 3.4 10.5 - - - -
76A PHE* 3.0 34.3 + - - +
78A MET* 5.6 3.4 - - - -
100A CYS 3.0 14.4 - - - -
101A CYS* 3.9 10.8 - - - -
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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