Contacts of the strand formed by residues 26 - 31 (chain M) in PDB entry 5A15
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 VAL 26 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L ALA* 5.0 8.7 - - + -
67L LYS 4.3 14.8 - - - +
68L ASP* 4.5 15.1 - - + -
69L SER 5.9 0.5 + - - -
74L PHE* 3.8 53.6 - - + -
24M PRO* 3.3 19.1 - - - +
25M GLU* 1.3 84.5 - - + +
27M VAL* 1.3 64.7 + - - +
28M GLU 4.0 1.0 + - - -
37M PHE* 4.3 16.2 - - + -
38M THR 3.6 9.4 - - - +
39M ARG* 4.2 4.3 - - + +
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Residues in contact with VAL 27 (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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23M PHE* 4.8 1.6 - - + -
24M PRO* 4.0 15.0 - - + +
26M VAL* 1.3 76.2 - - - +
28M GLU* 1.3 66.2 + - - +
29M LEU* 3.8 9.1 + - + +
36M TYR 3.9 0.2 - - - +
37M PHE* 3.5 5.2 - - - +
38M THR* 2.7 36.6 + - + +
40M HIS* 3.8 35.4 - - + -
43M LEU* 3.8 19.5 - - + -
55M PHE* 3.8 17.0 - - + -
73M PHE* 3.8 28.3 - - + -
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Residues in contact with GLU 28 (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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69L SER* 4.6 10.7 + - - -
24M PRO* 5.6 0.8 - - - +
26M VAL 4.0 1.4 + - - -
27M VAL* 1.3 72.3 - - - +
29M LEU* 1.3 60.9 + - - +
35M VAL* 4.4 1.5 - - + +
36M TYR 3.8 2.2 - - - -
37M PHE* 3.1 46.8 - - + -
72M ARG* 3.2 45.5 + - + +
73M PHE* 3.4 28.6 + - - -
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Residues in contact with LEU 29 (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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27M VAL* 4.2 9.6 - - + +
28M GLU* 1.3 75.0 - - - +
30M ASN* 1.3 58.3 + - - +
31M VAL* 4.1 7.9 - - + -
35M VAL* 3.4 10.6 - - - +
36M TYR* 2.6 47.0 + - + +
38M THR* 4.2 13.0 - - + -
43M LEU* 3.9 26.2 - - + -
51M LEU* 5.6 0.7 - - + -
55M PHE* 3.6 32.3 - - + -
72M ARG* 4.6 2.6 - - - -
73M PHE* 3.6 17.0 - - + +
75M ILE* 4.3 13.9 - - + -
82M PHE* 4.2 23.3 - - + -
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Residues in contact with ASN 30 (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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29M LEU* 1.3 74.4 - - - +
31M VAL* 1.3 60.2 + - - +
33M GLY* 3.0 31.3 + - - -
34M GLN 3.7 3.8 - - - -
35M VAL* 4.7 2.0 - - + +
68M ASP* 3.2 31.1 + - - +
72M ARG* 4.2 15.8 - - + +
73M PHE 2.7 15.5 + - - +
74M PHE* 3.2 15.8 - - + -
75M ILE 2.9 24.4 + - - -
37N PHE* 3.5 29.3 - - - -
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Residues in contact with VAL 31 (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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29M LEU* 4.5 8.3 - - + -
30M ASN* 1.3 74.4 + - - +
32M GLY* 1.3 58.0 + - - +
33M GLY 3.0 2.7 - - - -
34M GLN* 2.8 30.5 + - - +
36M TYR* 4.1 10.1 - - + -
75M ILE* 3.4 27.6 - - + +
77M ARG* 3.4 22.7 - - + +
78M ASP 3.7 14.4 - - - +
79M GLY* 3.1 17.6 - - - -
82M PHE* 3.9 39.9 - - + -
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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