Contacts of the strand formed by residues 118 - 122 (chain W) in PDB entry 5M32
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 PRO 118 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14W LYS* 3.3 25.6 - - + +
15W GLY 4.9 1.8 - - - +
16W LYS 3.6 23.8 - - - +
17W ASN* 4.1 11.4 - - - +
18W CYS 4.4 0.7 - - - +
19W VAL* 3.6 24.2 - - + -
110W GLY 3.4 7.2 - - - +
111W LEU* 3.7 11.4 - - + -
116W PHE 3.3 10.3 - - - +
117W LYS* 1.3 108.5 + - + +
119W PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 119 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14W LYS* 3.8 11.0 - - - +
19W VAL* 4.3 0.3 - - - +
83W PRO* 3.5 35.2 - - + -
84W TYR* 3.4 39.0 - + + -
87W MET* 5.0 7.9 - - + -
108W ILE* 4.1 6.2 - - + +
109W ALA* 3.9 0.2 - - - -
110W GLY 2.9 34.3 + - - +
112W ASP* 5.6 1.8 - - + -
117W LYS 4.4 7.4 - - - -
118W PRO* 1.3 77.2 - - - +
120W ILE* 1.3 78.1 + - - +
121W CYS* 4.5 15.5 - - + -
131W VAL* 5.2 9.0 - - + -
132W THR 4.3 6.7 - - - +
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Residues in contact with ILE 120 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W ALA* 3.7 18.2 - - + +
13W MET* 4.3 8.5 - - - +
14W LYS* 4.5 14.8 - - + -
19W VAL* 4.4 13.2 - - + -
108W ILE 3.3 3.8 - - - +
109W ALA* 3.7 26.2 - - + -
119W PHE* 1.3 87.1 - - - +
121W CYS* 1.3 61.4 + - - +
132W THR* 2.8 53.9 + - - +
134W ASP 4.2 0.7 - - - -
135W PHE* 3.6 42.4 - - - +
136W VAL* 3.7 4.7 - - + +
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Residues in contact with CYS 121 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87W MET* 3.5 41.5 - - + -
107W VAL* 3.2 9.2 - - - +
108W ILE* 2.8 38.8 + - + +
119W PHE* 4.5 8.5 - - + -
120W ILE* 1.3 76.0 - - - +
122W SER* 1.3 85.7 + - - +
123W LEU* 3.7 8.1 - - - -
130W MET 3.2 18.8 - - - +
131W VAL* 4.6 2.0 - - - -
136W VAL* 3.5 8.0 - - - +
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Residues in contact with SER 122 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V ALA 6.2 0.4 - - - -
105W GLU* 5.2 0.5 - - - +
106W PRO 3.9 5.6 - - - -
107W VAL* 4.0 11.4 - - - +
121W CYS* 1.3 80.3 - - - +
123W LEU* 1.3 73.3 + - - +
128W CYS 3.2 1.2 - - - +
130W MET* 2.9 43.9 + - - +
136W VAL* 3.7 22.0 - - - -
137W VAL 4.1 11.3 + - - -
138W SER* 5.0 1.9 - - - -
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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