Contacts of the strand formed by residues 37 - 41 (chain G) in PDB entry 1O18
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 37 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G PHE* 3.8 23.5 - - - -
33G ASP* 2.4 38.0 + - - +
34G ALA* 3.4 10.4 - - - +
36G SER* 1.4 72.7 - - - +
38G VAL* 1.3 71.1 + - - +
50G GLY 4.0 5.4 - - - -
51G THR* 4.7 6.3 - - - +
79G SER* 4.6 0.9 - - - -
80G MET* 3.9 22.3 + - - +
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Residues in contact with VAL 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ALA 5.1 1.8 - - - +
35G MLY 5.5 0.9 - - - +
36G SER 4.0 0.9 - - - +
37G SER* 1.3 84.9 - - - +
39G PHE* 1.3 77.8 + - - +
40G VAL* 4.6 3.8 - - + -
49G MLY 3.7 5.5 - - - +
50G GLY 2.7 41.7 + - - +
52G ILE* 3.3 37.0 - - + -
62G VAL* 5.2 1.6 - - + -
77G VAL* 4.0 23.6 - - + -
78G PHE 3.5 12.8 - - - +
79G SER* 4.4 6.5 - - - +
80G MET* 4.1 11.9 - - - +
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Residues in contact with PHE 39 (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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38G VAL* 1.3 86.2 - - - +
40G VAL* 1.3 62.4 + - - +
47G PHE* 5.3 0.4 - - + -
48G VAL 3.9 3.1 - - - -
49G MLY 3.7 39.9 - - + -
50G GLY 5.3 0.2 - - - -
78G PHE* 2.5 35.1 + - + +
79G SER 3.2 22.0 - - - -
80G MET* 4.0 22.0 - - + -
81G ASN* 5.0 2.0 - - - -
98G HIS* 4.4 2.0 - + - -
100G PRO* 3.7 29.2 - - + -
101G ALA* 3.9 20.9 - - + -
104G TYR* 3.5 49.6 - + + -
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Residues in contact with VAL 40 (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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38G VAL* 4.6 4.7 - - + -
39G PHE* 1.3 75.5 - - - +
41G VAL* 1.3 74.7 + - - +
42G HIS* 6.0 0.2 - - + -
47G PHE* 3.1 12.2 - - - -
48G VAL* 2.9 49.2 + - + +
49G MLY 5.5 2.9 - - - -
50G GLY 5.9 0.4 - - - +
62G VAL* 5.0 18.4 - - + -
63G MLY 6.0 0.9 - - - +
70G LEU* 5.9 7.0 - - + -
72G VAL* 3.5 25.1 - - + -
76G GLN 2.8 24.5 - - - +
77G VAL* 3.9 9.6 - - + -
78G PHE* 4.6 0.2 - - - -
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Residues in contact with VAL 41 (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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40G VAL* 1.3 91.9 - - + +
42G HIS* 1.3 76.0 + - - +
43G PRO* 4.4 6.7 - - + +
46G SER 3.9 5.8 - - - +
47G PHE* 4.0 17.9 - - + -
70G LEU* 4.9 6.2 - - - +
72G VAL* 4.1 13.0 - - + -
76G GLN* 2.9 48.2 + - + +
78G PHE* 4.7 2.2 - - + -
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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