Contacts of the strand formed by residues 64 - 68 (chain X) 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 TYR 64 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X VAL* 3.9 23.8 - - + -
34X TYR 3.7 4.9 - - - -
35X ARG* 4.6 3.4 - - + -
36X PHE* 3.6 10.1 - - - -
58X CYS 4.1 11.9 - - - -
59X TYR* 3.1 30.7 - - - -
60X ASN* 3.1 30.7 + - + -
61X ASP 4.6 5.4 - - - -
63X LYS* 1.3 78.5 - - - +
65X GLN* 1.3 65.8 + - - +
84X LEU* 4.4 10.0 - - - +
85X VAL* 4.1 39.8 + - + +
88X ALA* 3.9 22.2 - - + +
104X MET* 3.3 22.5 - - + +
106X LEU* 4.3 9.2 - - + -
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Residues in contact with GLN 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X VAL* 3.6 1.2 - - - -
34X TYR* 2.6 52.9 + - + +
36X PHE* 3.2 22.8 - - + -
64X TYR* 1.3 76.1 - - - +
66X VAL* 1.3 62.0 + - - +
67X TRP* 3.4 22.1 - - + +
82X HIS* 4.3 19.2 + - + -
83X ARG 4.0 6.7 - - - +
84X LEU* 4.0 23.5 - - + +
170Z LYS 5.2 0.9 - - - +
171Z ALA 3.8 19.6 + - - +
172Z HIS 5.5 0.2 - - - -
173Z ILE* 3.6 20.5 - - - +
224Z MET* 5.0 2.0 - - - +
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Residues in contact with VAL 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31X VAL* 3.4 23.8 - - + -
32X ALA 3.6 2.2 - - - +
33X VAL* 4.4 14.6 - - + -
52X VAL* 4.2 7.2 - - + -
65X GLN* 1.3 74.8 - - - +
67X TRP* 1.3 60.6 + - - +
68X LEU* 3.8 13.5 + - + +
82X HIS* 3.2 4.0 - - - +
83X ARG 2.9 43.2 + - - +
85X VAL* 3.7 23.7 - - + +
106X LEU* 4.1 16.6 - - + -
108X LEU* 3.8 25.1 - - + -
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Residues in contact with TRP 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLY* 4.1 31.4 - - - -
11B GLU 5.7 0.7 - - - -
31X VAL* 3.2 3.9 - - - +
32X ALA* 2.8 52.4 + - + +
34X TYR* 3.4 49.8 - + + -
41X GLN* 4.3 17.9 - - - -
65X GLN* 3.4 24.3 - - + +
66X VAL* 1.3 78.6 - - - +
68X LEU* 1.3 60.2 + - - +
69X GLY 4.2 1.2 + - - +
81X GLN 3.5 6.1 - - - +
82X HIS* 3.8 17.1 - - + +
95Z LEU* 4.8 0.4 - - - -
173Z ILE* 4.5 11.6 - - + +
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Residues in contact with LEU 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X HIS 4.9 0.7 - - - +
31X VAL* 3.6 22.0 - - + -
46X LEU* 3.8 33.7 - - + -
52X VAL* 4.5 2.0 - - + -
66X VAL* 3.8 15.7 - - + +
67X TRP* 1.3 73.5 - - - +
69X GLY* 1.3 60.3 + - - +
80X ASP* 3.6 6.1 - - - +
81X GLN* 2.7 54.9 + - + +
83X ARG* 3.9 28.5 - - + -
108X LEU* 4.7 2.7 - - + -
112X ALA* 3.9 20.2 - - + -
118X VAL* 4.3 11.2 - - + -
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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