Contacts of the strand formed by residues 141 - 145 (chain O) in PDB entry 3A0B
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 ARG 141 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A PRO* 4.4 7.3 - - - +
57A PRO* 2.8 59.1 + - + +
66A PRO* 4.2 5.9 - - - +
103A ASP 4.8 1.4 + - - -
106A LEU* 5.3 0.2 - - - +
107A TYR* 3.1 56.4 - - - +
310D GLU* 5.6 1.6 - - - +
97O VAL* 4.6 2.5 - - - +
133O THR* 4.6 6.5 - - + -
134O VAL 3.8 11.4 - - - -
135O GLN* 3.0 28.7 + - - +
139O GLY 3.9 6.5 + - - +
140O GLU* 1.3 79.2 - - - +
142O ILE* 1.3 61.2 + - - +
143O PRO* 3.3 11.3 - - + +
254O HIS* 6.0 0.3 + - - -
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Residues in contact with ILE 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O VAL* 4.4 18.2 - - + -
133O THR* 3.6 2.5 - - - -
134O VAL* 3.0 41.6 + - + +
136O MET* 3.1 43.3 - - + +
140O GLU* 3.8 9.6 - - + +
141O ARG* 1.3 83.6 - - - +
143O PRO* 1.3 65.9 - - + +
144O LEU* 4.7 1.7 - - + +
247O SER* 3.8 26.7 - - - -
257O HIS* 4.2 29.8 - - + +
259O VAL* 5.0 2.5 - - + -
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Residues in contact with PRO 143 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TYR* 5.8 0.2 - - - +
310D GLU* 5.0 11.0 - - - +
132O VAL 3.6 5.2 - - - +
133O THR* 3.3 22.2 - - + +
141O ARG 3.3 11.2 - - - +
142O ILE* 1.3 88.7 - - + +
144O LEU* 1.3 59.8 + - - +
177O TYR* 3.8 22.7 - - + +
247O SER* 3.5 4.9 - - - -
248O ASP* 3.1 44.3 + - + +
254O HIS* 5.9 4.5 - - + +
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Residues in contact with LEU 144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O PHE* 4.2 9.2 - - + -
131O PRO* 3.4 2.4 - - - +
132O VAL* 2.9 57.7 + - + +
133O THR* 4.6 3.8 - - - +
134O VAL* 5.3 2.9 - - + -
142O ILE* 4.7 3.8 - - + +
143O PRO* 1.3 77.0 - - + +
145O LEU* 1.3 64.2 + - - +
146O PHE 3.9 6.9 + - - +
177O TYR* 3.7 8.1 - - - -
245O GLN* 4.5 12.1 - - + +
246O LEU 4.6 2.0 - - - +
247O SER* 4.0 19.7 - - - +
259O VAL* 3.5 26.9 - - + -
261O ILE* 3.4 31.4 - - + -
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Residues in contact with LEU 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C GLN* 3.4 18.4 - - - +
336C GLY 5.4 0.7 - - - +
129O PHE* 5.4 3.8 - - + -
130O GLN 4.4 4.9 - - - +
131O PRO* 3.9 19.1 - - + -
144O LEU* 1.3 79.5 - - - +
146O PHE* 1.3 55.3 + - - +
147O THR* 2.8 19.8 + - + +
174O VAL* 4.0 18.4 - - + -
175O PRO* 4.5 10.1 - - + -
176O SER* 3.1 35.9 - - - +
177O TYR* 3.9 20.4 - - + +
245O GLN* 2.6 21.3 + - - +
246O LEU 4.8 6.7 - - - +
247O SER 4.9 4.3 - - - +
248O ASP* 6.1 0.2 - - - -
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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