Contacts of the strand formed by residues 108 - 112 (chain G) 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 ALA 108 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69G ASN 3.0 7.8 + - - +
70G VAL* 3.9 23.3 - - + -
71G ALA* 3.0 24.8 + - - +
90G VAL* 5.2 0.2 - - - +
106G PRO 4.3 0.4 - - - -
107G VAL* 1.3 79.8 - - - +
109G VAL* 1.3 62.6 + - - +
110G ALA 4.1 0.2 - - - -
237G ASP* 3.3 10.5 - - - +
238G MET* 3.9 16.4 - - + -
460G ARG* 3.6 26.7 + - - +
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Residues in contact with VAL 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G ALA* 3.8 7.9 - - + +
73G LEU* 4.5 10.8 - - + -
87G ILE* 4.0 24.2 - - + -
90G VAL* 4.7 18.6 - - + -
91G ARG* 4.4 27.1 - - + +
107G VAL 4.8 4.7 - - - +
108G ALA* 1.3 78.0 - - - +
110G ALA* 1.3 63.1 + - - +
236G VAL* 3.7 28.3 - - + +
237G ASP* 2.9 40.7 + - - +
238G MET* 3.4 7.5 + - - -
460G ARG* 5.8 1.1 - - - -
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Residues in contact with ALA 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G VAL* 3.8 9.0 - - + -
71G ALA 2.8 16.4 + - - +
72G ARG* 4.0 1.6 - - - -
73G LEU* 2.8 35.7 + - - +
108G ALA 4.1 0.2 - - - -
109G VAL* 1.3 78.4 - - - +
111G LEU* 1.3 56.1 + - - +
238G MET* 3.5 16.2 - - + +
240G PHE* 3.4 38.4 - - + -
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Residues in contact with LEU 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G LEU 4.0 1.8 - - - -
75G PHE* 3.6 34.1 - - + -
87G ILE* 6.3 0.7 - - + -
109G VAL 4.3 0.2 + - - -
110G ALA* 1.3 72.1 - - - +
112G ASP* 1.3 56.1 + - - +
113G THR* 3.8 28.7 - - + +
227G ASP* 3.5 27.8 - - + +
228G LEU* 4.6 8.5 - - + -
230G PHE* 4.9 0.4 - - + -
231G GLY* 3.7 23.8 - - - +
236G VAL* 4.5 15.6 - - + +
238G MET 3.0 12.6 + - - +
239G VAL* 3.4 12.0 - - + +
240G PHE* 2.7 33.4 + - - +
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Residues in contact with ASP 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G ARG* 2.9 42.6 + - + +
73G LEU 2.7 22.4 + - - +
74G ASN* 3.0 8.2 - - - +
75G PHE* 2.8 33.1 + - - +
110G ALA 3.9 0.2 + - - -
111G LEU* 1.3 74.6 - - - +
113G THR* 1.3 64.4 + - - +
240G PHE* 3.4 21.3 - - + +
269G LYS* 3.2 14.4 + - - +
532G K 2.8 27.2 - - - -
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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