Contacts of the strand formed by residues 79 - 83 (chain M) in PDB entry 4XX1
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 LEU 79 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M CYS* 3.0 56.7 + - + +
29M PHE* 4.1 15.3 - - + -
34M MET* 3.6 24.0 - - + +
35M HIS 4.2 3.6 - - - +
36M TRP* 3.6 28.5 - - + +
51M ILE* 3.5 31.6 - - + -
70M ILE* 4.0 11.9 - - + -
71M SER 4.0 11.2 - - - +
72M ARG* 4.4 4.9 - - + +
78M THR* 1.3 76.7 - - - +
80M TYR* 1.3 66.0 + - - +
96M CYS* 4.1 2.0 - - - -
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Residues in contact with TYR 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M LEU 3.3 8.3 + - - -
19M ARG* 3.2 25.2 - - + -
20M LEU* 2.8 62.3 + - + +
21M SER* 3.7 4.5 - - - -
36M TRP* 3.4 22.0 - + - +
70M ILE* 3.4 4.9 - - - -
71M SER* 2.5 45.1 + - - -
78M THR* 5.9 1.6 - - - -
79M LEU* 1.3 77.3 - - - +
81M LEU* 1.3 100.4 + - + +
82M GLN* 3.7 6.1 + - - -
83M MET* 3.5 14.1 - - + +
94M TYR* 5.9 0.4 - + - -
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Residues in contact with LEU 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36M TRP* 3.3 38.8 - - + -
48M VAL* 3.7 20.6 - - + -
49M ALA* 3.9 7.9 - - + -
60M TYR* 6.3 0.2 - - + -
68M PHE* 3.7 30.5 - - + -
69M THR 3.4 5.6 - - - +
70M ILE* 3.4 21.3 - - + +
80M TYR* 1.3 110.5 + - + +
82M GLN* 1.3 67.8 + - - +
83M MET* 3.4 12.7 - - + +
94M TYR* 5.2 3.6 - - + -
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Residues in contact with GLN 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M ARG* 3.2 47.2 + - - +
68M PHE* 3.1 5.5 - - - +
69M THR* 2.5 64.2 + - - +
71M SER* 6.0 0.2 - - - -
80M TYR* 3.7 5.0 + - - -
81M LEU* 1.3 71.2 - - - +
83M MET* 1.3 57.5 + - - +
84M ASP* 2.2 34.7 + - - +
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Residues in contact with MET 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M ARG* 2.8 8.6 + - - -
17M SER* 2.6 30.6 + - - -
18M LEU* 3.5 40.1 + - + +
19M ARG* 2.9 8.5 - - - +
20M LEU* 5.6 0.9 - - + -
68M PHE* 3.6 40.4 - - + -
80M TYR* 3.5 10.1 - - - +
81M LEU* 3.4 20.2 - - + +
82M GLN* 1.3 71.3 - - - +
84M ASP* 1.3 55.4 + - - +
86M LEU* 4.4 15.3 - - + +
94M TYR* 3.3 38.1 - - + +
122M VAL* 5.0 2.7 - - + -
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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