Contacts of the strand formed by residues 142 - 146 (chain A) in PDB entry 3RSG
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLU* 6.1 1.8 - - + -
35A LEU* 4.0 28.9 - - + -
41A TYR* 5.9 4.0 - - + -
110A ASP 3.4 13.3 + - - +
111A VAL* 3.4 18.2 - - + +
112A VAL 2.9 28.1 + - - +
140A GLY 4.0 0.2 + - - -
141A LYS* 1.3 71.8 - - - +
143A VAL* 1.3 61.9 + - - +
144A VAL* 4.4 11.7 - - + -
167A ASP* 3.4 16.4 - - + +
168A LEU* 6.3 0.4 - - + -
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 3.5 12.1 - - + +
114A ASP* 4.5 5.2 - - + -
136A VAL* 3.7 31.0 - - + +
137A ASN* 5.9 0.4 - - - +
141A LYS* 3.4 18.2 - - + +
142A VAL* 1.3 75.5 - - - +
144A VAL* 1.3 66.4 + - - +
145A SER* 4.1 4.3 - - - +
164A VAL* 3.6 30.5 - - + -
165A LYS 3.7 16.8 - - - +
166A ALA* 3.7 3.3 - - - -
167A ASP* 2.8 40.8 + - - +
168A LEU 3.2 7.6 + - - +
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Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 4.1 16.2 - - + -
31A MET* 3.8 43.3 - - + -
34A GLU* 6.3 0.7 - - + -
35A LEU* 5.3 2.7 - - + -
111A VAL* 4.1 12.3 - - + -
112A VAL 2.9 9.9 + - - +
113A VAL* 3.3 7.5 - - + +
114A ASP* 2.8 30.9 + - - -
142A VAL* 4.4 10.3 - - + -
143A VAL* 1.3 77.4 - - - +
145A SER* 1.3 62.2 + - - +
146A VAL 3.9 0.2 + - - -
168A LEU* 3.2 29.2 - - + +
170A VAL* 4.7 2.9 - - + -
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Residues in contact with SER 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 5.6 0.2 - - - +
114A ASP* 2.6 28.3 + - - +
143A VAL 4.1 0.6 - - - -
144A VAL* 1.3 76.0 - - - +
146A VAL* 1.3 62.8 + - - +
147A ASP 3.5 0.3 + - - -
148A VAL 4.1 0.7 - - - -
149A PRO* 3.4 24.8 - - - +
164A VAL* 3.5 6.2 - - - +
166A ALA* 3.5 13.6 - - - +
168A LEU 2.9 8.5 + - - +
169A THR* 3.4 15.7 - - - +
170A VAL* 3.0 28.6 + - - +
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 4.2 19.5 - - + -
52A ASN* 3.0 25.0 + - - +
55A ASP* 3.7 26.2 - - + -
56A GLY* 4.9 0.7 - - - -
59A VAL* 4.8 6.5 - - + -
113A VAL* 3.8 28.9 - - + -
114A ASP 2.9 15.7 + - - +
115A ALA* 4.1 10.8 - - + -
145A SER* 1.3 72.9 - - - +
147A ASP* 1.3 58.9 + - - +
148A VAL 3.0 5.0 + - - -
170A VAL 4.1 1.8 - - - -
172A PHE* 3.9 16.4 - - + -
491A K 2.9 19.4 - - - -
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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