Contacts of the strand formed by residues 65 - 68 (chain G) in PDB entry 1SGF
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 LYS 65 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G VAL* 3.6 1.6 - - - +
34G TYR* 2.9 40.3 + - + +
36G TYR* 2.9 36.3 + - - +
63G ASN* 4.2 10.2 + - - +
64G TYR* 1.3 76.4 - - - +
66G VAL* 1.3 65.4 + - - +
67G TRP 4.3 0.4 - - - -
82G HIS* 4.7 12.1 - - + -
83G ARG 3.8 5.4 - - - +
84G PHE* 3.7 36.0 - - + +
74Z PHE* 3.5 26.0 - - + -
153Z ASP* 2.7 37.3 + - - +
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Residues in contact with VAL 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G VAL* 3.5 27.1 - - + -
32G ALA 3.7 2.9 - - - +
33G VAL* 4.7 2.7 - - + -
52G VAL* 4.2 6.5 - - + -
65G LYS* 1.3 81.9 - - - +
67G TRP* 1.3 61.1 + - - +
68G LEU* 3.7 20.3 + - + +
82G HIS* 3.3 6.3 - - - +
83G ARG 2.8 43.0 + - - +
85G VAL* 3.7 21.8 - - + -
106G LEU* 4.2 15.9 - - + -
108G LEU* 4.0 19.5 - - + -
74Z PHE* 6.5 0.2 - - - -
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Residues in contact with TRP 67 (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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30G HIS 4.6 0.2 - - - +
31G VAL* 3.6 7.6 - - - +
32G ALA* 3.0 39.3 + - + +
34G TYR* 3.5 40.0 - + + -
65G LYS 4.3 0.2 - - - -
66G VAL* 1.3 72.1 - - - +
68G LEU* 1.3 60.4 + - - +
69G GLY 4.3 0.3 + - - -
70G LYS* 3.6 38.3 + - + +
73G LEU* 3.5 42.0 - - + -
80G ALA* 4.7 5.2 - - + +
81G GLN 3.2 18.7 + - - -
82G HIS* 3.8 13.9 - - + +
141G TRP* 5.8 0.9 - - - -
67Z TRP* 5.2 2.5 - + - -
73Z LEU 4.5 9.6 - - - -
74Z PHE* 3.9 43.4 + + + -
75Z LYS 6.0 0.9 - - - -
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Residues in contact with LEU 68 (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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28G PRO 5.4 2.2 - - - +
31G VAL* 3.7 20.6 - - + -
46G LEU* 3.6 37.2 - - + -
52G VAL* 5.1 0.4 - - + -
66G VAL* 3.7 17.0 + - + +
67G TRP* 1.3 76.1 - - - +
69G GLY* 1.3 63.9 + - - +
70G LYS* 3.6 1.6 - - - -
80G ALA* 3.3 4.9 - - - +
81G GLN* 3.0 48.6 + - + +
83G ARG* 3.7 30.3 - - + -
108G LEU* 4.5 3.1 - - + -
112G ALA* 4.1 13.7 - - + -
118G VAL* 4.2 14.7 - - + +
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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