Contacts of the strand formed by residues 36 - 40 (chain G) in PDB entry 5A0Q
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 ALA 36 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G SER 3.4 3.0 + - - -
35G THR* 1.3 77.2 - - - +
37G ILE* 1.3 62.9 + - - +
48G GLY 3.5 5.6 - - - -
49G VAL* 3.5 26.9 - - + -
76G ALA 4.4 1.3 - - - +
77G VAL 4.1 11.9 - - - +
78G ALA* 4.5 4.3 - - + -
136G MET* 3.4 25.6 - - + -
164G ALA* 3.3 1.4 - - - -
165G ILE 3.1 29.1 + - - +
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Residues in contact with ILE 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G THR* 4.9 3.1 - - - +
36G ALA* 1.3 77.8 - - - +
38G GLY* 1.4 61.7 + - - +
39G ILE* 4.1 9.0 - - + -
46G VAL 3.7 0.2 - - - +
47G PHE 3.7 0.2 - - - -
48G GLY 2.7 33.7 + - - +
136G MET* 3.8 1.8 - - - -
163G CYS 3.4 15.3 - - - +
164G ALA* 4.1 14.8 - - + -
172G ALA* 4.7 2.5 - - + -
176G ILE* 4.3 14.6 - - + -
193G VAL* 3.5 14.0 - - + +
196G ILE* 3.6 45.1 - - + -
197G ILE* 3.7 35.9 - - + -
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Residues in contact with GLY 38 (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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37G ILE* 1.4 73.3 - - - +
39G ILE* 1.3 66.8 + - - +
45G VAL* 4.5 6.3 - - - -
46G VAL 3.3 9.0 - - - -
47G PHE* 3.9 7.6 - - - -
136G MET* 3.1 20.2 - - - -
148G LEU* 3.7 7.6 - - - -
163G CYS 2.7 28.1 + - - +
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Residues in contact with ILE 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ILE* 4.1 6.3 - - + -
38G GLY* 1.3 78.9 - - - +
40G ARG* 1.4 76.2 + - - +
41G CYS* 3.6 2.9 + - - +
44G GLY 3.7 1.0 - - - +
45G VAL* 3.4 21.0 - - - +
46G VAL 3.3 10.8 + - - +
148G LEU* 3.8 3.7 - - - +
162G GLY* 4.2 2.5 - - - -
176G ILE* 3.7 14.6 - - + -
179G LEU* 3.5 26.5 - - + -
181G MET* 3.5 24.2 - - + -
189G ILE* 3.9 21.7 - - + +
193G VAL* 3.4 27.4 - - + +
196G ILE* 3.7 12.6 - - + -
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Residues in contact with ARG 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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39G ILE* 1.4 72.7 - - - +
41G CYS* 1.3 58.5 + - - +
44G GLY 4.0 2.0 - - - -
45G VAL* 4.1 8.5 - - + -
146G ALA* 3.5 38.1 + - + +
147G GLN* 4.1 20.7 + - - +
148G LEU* 3.3 13.9 - - + +
160G TYR 3.5 19.5 + - - +
161G TRP* 3.1 66.0 + - - +
181G MET* 1.6 40.9 - - - +
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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