Contacts of the strand formed by residues 62 - 67 (chain G) in PDB entry 43C9
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 62 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G GLN* 4.2 8.1 - - - -
47G LEU* 3.9 27.1 - - + -
48G VAL* 4.9 4.5 - - + +
54G ARG* 2.4 35.1 + - - +
58G VAL* 3.6 14.6 - - + -
59G PRO* 3.2 32.5 + - + +
60G ASP 3.0 1.0 - - - -
61G ARG* 1.3 95.0 - - + +
63G ILE* 1.3 56.5 + - - +
64G GLY 4.1 1.1 + - - -
73G LEU* 4.7 8.5 - - + -
74G THR 3.4 2.5 - - - -
75G ILE* 3.9 31.6 - - + -
82G ASP* 3.3 31.4 - - - -
86G TYR* 4.0 16.2 - + - -
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Residues in contact with ILE 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G SER 6.1 0.2 - - - +
54G ARG* 3.8 15.3 - - - +
60G ASP 3.6 17.5 - - - +
61G ARG 4.2 8.1 - - - +
62G PHE* 1.3 78.1 - - - +
64G GLY* 1.3 70.5 + - - +
65G SER* 3.8 5.0 + - - -
72G THR 3.7 0.7 - - - +
73G LEU* 3.4 3.3 - - - +
74G THR* 2.8 57.7 + - + +
76G SER* 4.4 16.8 - - - +
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Residues in contact with GLY 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G TRP* 4.9 3.6 - - - -
48G VAL* 4.4 11.3 - - - +
51G ALA 3.1 22.3 - - - +
52G SER* 3.6 22.6 + - - +
62G PHE 4.1 2.0 + - - -
63G ILE* 1.3 79.5 - - - +
65G SER* 1.3 59.9 + - - -
72G THR 3.7 4.5 - - - -
73G LEU* 4.0 11.0 - - - +
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Residues in contact with SER 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G TRP* 5.2 1.0 + - - -
51G ALA* 4.0 6.8 - - - +
52G SER* 4.9 2.7 - - - -
63G ILE* 5.1 6.7 - - - -
64G GLY* 1.3 75.1 - - - -
66G GLY* 1.3 66.7 + - - +
71G PHE* 3.7 10.2 - - - +
72G THR* 2.9 43.9 + - - +
74G THR* 4.2 5.8 + - - -
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Residues in contact with GLY 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G ASN* 4.4 3.6 + - - -
51G ALA* 4.5 4.9 - - - +
52G SER* 5.4 1.9 + - - -
65G SER* 1.3 82.5 + - - +
67G SER* 1.3 65.3 + - - -
70G ASP 3.2 15.0 - - - -
71G PHE* 3.8 10.5 - - - -
72G THR* 4.5 1.6 - - - -
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Residues in contact with SER 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G LEU* 4.2 11.1 - - - -
31G ASN* 3.4 16.4 + - - +
66G GLY* 1.3 76.6 - - - -
68G GLY* 1.3 63.2 + - - +
69G THR 2.7 17.8 + - - -
70G ASP* 3.1 15.4 + - - +
71G PHE* 3.7 11.6 - - - -
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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