Contacts of the strand formed by residues 70 - 74 (chain B) in PDB entry 3SRF
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 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B ILE 3.0 3.2 + - - -
47B ILE* 3.2 36.5 - - + -
48B CYS 2.8 27.4 + - - -
68B MET* 3.6 7.7 - - - +
69B ASN* 1.3 86.5 - - + +
71B ALA* 1.3 62.1 + - - +
72B ARG 3.9 0.2 - - - -
108B ALA* 3.3 25.6 - - + +
110B ALA* 3.8 23.6 - - + -
238B MET* 4.2 13.5 - - + -
240B PHE* 4.7 0.9 - - + -
357B CYS* 5.6 2.5 - - - -
463B HIS* 4.2 18.2 - - + +
464B LEU* 5.3 2.5 - - + +
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Residues in contact with ALA 71 (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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48B CYS 3.3 4.9 - - - -
50B ILE* 3.7 22.7 - - + -
68B MET* 4.2 11.2 - - + -
70B VAL* 1.3 72.7 - - - +
72B ARG* 1.3 62.6 + - - +
73B LEU* 3.7 8.2 - - + +
90B VAL* 4.2 25.1 - - + -
107B VAL* 4.3 1.2 - - + +
108B ALA 2.9 13.4 + - - +
109B VAL* 3.9 2.2 - - + -
110B ALA 3.0 24.9 + - - +
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Residues in contact with ARG 72 (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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47B ILE* 3.8 14.3 - - + +
48B CYS 2.9 8.9 + - - -
49B THR* 3.1 42.8 - - + +
50B ILE 3.0 24.3 + - - -
70B VAL 3.9 1.2 + - - -
71B ALA* 1.3 71.6 - - - +
73B LEU* 1.3 65.0 + - - +
74B ASN* 3.7 26.0 + - - +
110B ALA* 3.7 7.0 - - - +
112B ASP* 2.8 50.3 + - + -
240B PHE* 3.7 10.3 - - + -
359B MET* 3.6 27.1 - - - +
361B SER* 3.8 9.5 - - - -
532B K 3.9 5.5 - - - -
534B PYR 4.0 15.9 + - - +
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Residues in contact with LEU 73 (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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50B ILE* 5.0 6.1 - - + +
71B ALA* 3.7 24.0 - - + +
72B ARG* 1.3 75.4 - - - +
74B ASN* 1.3 61.1 + - - +
75B PHE* 3.3 21.3 - - + -
83B HIS* 3.6 32.5 - - + +
86B THR* 4.0 24.2 - - + -
87B ILE* 3.6 32.3 - - + -
90B VAL* 5.1 3.8 - - + -
109B VAL* 4.3 13.5 - - + -
110B ALA 2.9 17.3 + - - +
111B LEU* 5.0 0.2 - - - -
112B ASP 3.0 23.2 + - - -
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Residues in contact with ASN 74 (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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49B THR* 5.6 2.7 - - - -
50B ILE 5.4 2.8 + - - -
72B ARG* 3.7 30.5 + - - +
73B LEU* 1.3 68.5 - - - +
75B PHE* 1.3 61.6 + - - +
76B SER* 3.2 12.8 + - - -
77B HIS* 3.1 49.8 + - - +
83B HIS* 3.3 9.6 - - - -
112B ASP* 3.8 7.8 - - - +
532B K 3.2 21.0 - - - -
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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