Contacts of the strand formed by residues 62 - 67 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E PHE* 3.4 20.8 - - - -
55E THR* 4.1 3.0 - - - +
60E ILE 2.9 17.6 + - - -
61E PRO* 1.3 73.6 + - - +
63E TRP* 1.3 62.9 + - - +
103E GLN* 3.5 6.5 - - - +
104E MET* 2.8 40.7 + - - +
121E HIS* 4.5 1.3 - - - -
122E SER* 3.3 10.0 - - - -
123E SER* 3.9 10.8 - - - -
124E ILE* 4.0 18.6 - - - -
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Residues in contact with TRP 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LEU 3.0 28.2 + - - -
24E HIS 4.1 0.2 - - - -
25E TRP* 3.3 35.1 - + + +
28E ALA* 4.2 6.5 - - + -
39E LEU* 4.1 6.3 - - + +
62E SER* 1.3 73.6 - - - +
64E ILE* 1.3 62.1 + - - +
101E CYS* 3.5 35.4 - - + -
102E ILE 3.3 18.8 - - - -
103E GLN* 4.1 10.3 - - + -
115E THR* 3.4 14.8 - - - -
116E PRO 3.3 24.9 - - - -
117E CYS* 3.7 8.1 - - - -
119E HIS 3.2 20.6 + - - -
121E HIS* 3.7 28.1 - + + +
122E SER 2.8 15.0 + - - +
123E SER* 3.5 8.5 - - - -
124E ILE 3.1 25.6 + - - -
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Residues in contact with ILE 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E TRP* 3.0 21.1 + - - -
39E LEU* 3.8 7.6 - - - -
40E ALA* 2.5 31.0 - - + +
41E SER* 4.5 0.7 - - - -
42E ILE* 3.0 24.7 - - + -
51E VAL* 5.0 0.7 - - + -
62E SER 3.7 0.4 + - - +
63E TRP* 1.3 79.5 - - - +
65E GLY* 1.3 60.5 + - - +
66E GLY 3.1 6.9 + - - +
77E TRP* 3.2 23.6 - - + -
102E ILE* 3.2 22.4 + - + +
104E MET* 2.9 47.8 - - + -
112E TRP* 4.9 3.4 - - + +
124E ILE* 4.0 12.6 - - + -
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Residues in contact with GLY 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E TRP* 4.3 9.6 - - - -
39E LEU* 3.3 27.4 - - - +
40E ALA 2.8 9.7 + - - -
64E ILE* 1.3 80.3 - - - +
66E GLY* 1.3 55.7 + - - -
67E THR* 4.8 0.2 - - - +
76E PHE 3.6 0.9 - - - +
77E TRP* 3.3 9.3 - - - -
78E MET* 2.9 33.8 + - - +
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Residues in contact with GLY 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E ILE 3.1 6.2 + - - +
65E GLY* 1.3 76.8 - - - +
67E THR* 1.3 70.7 + - - +
76E PHE 3.3 9.0 - - - -
77E TRP* 3.4 18.9 - - - -
83E MET* 4.3 1.6 - - - -
101E CYS* 3.7 0.2 - - - -
102E ILE* 2.9 39.4 + - - +
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Residues in contact with THR 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E TRP* 3.6 35.2 - - + -
65E GLY 4.8 0.7 - - - +
66E GLY* 1.3 82.2 - - - +
68E ASP* 1.3 61.4 + - - +
69E CYS* 3.3 22.2 + - - +
70E GLN* 4.2 10.0 + - - +
74E ARG 3.8 0.7 - - - +
75E TRP* 3.5 10.2 - - - -
76E PHE* 3.0 34.7 + - - +
78E MET* 5.6 3.0 - - + -
100E CYS 3.0 15.0 - - - -
101E CYS* 3.9 9.6 - - - -
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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