Contacts of the strand formed by residues 108 - 113 (chain B) in PDB entry 5M61
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 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LYS* 2.8 53.5 + - + -
85B GLY 3.6 7.8 + - - +
88B LEU* 4.2 11.4 - - + -
104B MET* 3.9 28.0 - - + -
106B ASP 3.5 1.3 + - - +
107B ASP* 1.3 75.0 - - - +
109B THR* 1.3 57.4 + - - +
110B PHE 3.4 22.7 - - - +
111B TRP* 4.0 10.8 - - + -
121B LEU* 4.2 15.9 - - + -
122B VAL 3.5 10.8 - - - +
123B THR* 4.4 7.2 - - + -
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Residues in contact with THR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LYS* 5.0 2.9 - - - -
107B ASP* 3.6 4.2 + - - -
108B VAL* 1.3 73.3 - - - +
110B PHE* 1.3 62.1 + - + +
122B VAL* 2.7 35.3 + - + +
123B THR 3.9 13.9 - - - +
124B ASP* 4.3 14.4 + - - +
144B ARG* 4.2 7.6 - - - +
153B ILE* 4.4 9.4 - - + +
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 4.1 18.2 - + - -
83B LYS* 5.4 0.9 - - - +
108B VAL* 3.4 3.4 - - - +
109B THR* 1.3 81.6 - - - +
111B TRP* 1.3 74.4 + - - +
112B LYS* 4.0 26.2 - - + -
120B ALA* 6.5 0.2 - - + -
122B VAL* 2.8 42.4 + - + +
153B ILE* 3.6 42.2 - - + +
154B ILE 3.8 16.8 - - - -
155B ASN* 3.7 17.7 - - - -
156B TYR* 3.9 24.5 - - + -
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Residues in contact with TRP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B GLU* 4.8 1.4 - - - +
70B SER* 2.8 27.9 + - - -
72B ILE* 3.6 25.5 - - + +
81B ALA* 3.5 38.6 - - + -
82B LEU* 3.4 22.4 - - - -
83B LYS* 3.5 40.2 - - + +
88B LEU* 4.1 21.5 - - + -
89B GLN 4.9 0.2 - - - -
90B ILE* 5.2 0.2 - - + -
108B VAL* 4.0 7.4 - - + -
110B PHE* 1.3 89.4 - - - +
112B LYS* 1.3 64.4 + - - +
119B VAL* 3.9 9.6 - - + -
120B ALA 3.1 16.4 - - - +
121B LEU* 3.6 20.4 - - + -
130B TRP* 5.2 5.4 - + - -
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Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B MET 4.6 4.9 + - - -
33B GLU* 3.4 38.9 + - - +
72B ILE* 3.8 8.2 - - - +
110B PHE* 4.0 19.5 - - + -
111B TRP* 1.3 79.9 - - - +
113B TRP* 1.3 75.3 + - - +
114B ILE* 3.4 3.9 + - + -
119B VAL* 4.1 1.3 - - - -
120B ALA* 2.9 31.1 + - + +
155B ASN* 3.8 20.4 - - - +
156B TYR* 3.7 21.3 - - + +
157B ARG* 6.1 0.7 - - - -
305B VAL* 5.6 4.2 - - - +
306B THR 5.0 7.4 + - - -
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Residues in contact with TRP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B GLU* 2.8 22.2 + - + +
72B ILE* 3.1 32.5 + - + +
73B MET 3.1 19.7 - - - -
74B ASN* 3.3 40.6 - - + +
75B PRO* 3.5 25.9 - - + +
79B VAL* 4.4 14.6 - - + -
81B ALA* 4.3 12.8 - - + -
90B ILE* 4.7 1.8 - - + -
112B LYS* 1.3 85.5 + - - +
114B ILE* 1.3 58.5 + - - +
115B SER 3.5 7.0 - - - +
117B ASN 4.0 0.7 - - - -
118B THR 3.6 21.8 - - - -
119B VAL* 3.4 31.6 - - + +
132B MET* 3.8 31.2 - - + -
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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