Contacts of the strand formed by residues 44 - 48 (chain A) in PDB entry 3GSB
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 PHE 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.5 27.8 - - + -
43A VAL* 1.3 87.1 - - - +
45A ASP* 1.3 61.5 + - - +
46A ARG 4.7 1.1 - - - +
47A VAL* 3.7 22.7 - - + -
52A ALA* 3.5 25.6 - - + -
53A TRP 3.7 5.8 - - - +
54A ASP* 3.9 2.9 - - - +
55A VAL* 4.3 2.9 - - - +
60A TYR* 5.4 4.9 - + - -
62A ASP* 4.2 8.1 - - - -
399A TYR* 3.6 42.0 - + - -
93B PHE* 3.6 40.7 - - + -
95B ALA* 3.5 21.8 - - + -
96B PRO 3.2 10.1 + - - +
97B CYS* 4.2 3.8 - - - +
98B ALA 4.9 1.0 + - - -
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Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 1.3 75.6 - - - +
46A ARG* 1.3 86.3 + - - +
53A TRP 2.7 16.8 + - - +
54A ASP 3.8 13.9 - - - +
55A VAL* 4.3 16.0 - - - +
89B LYS* 3.0 36.4 + - - +
93B PHE* 3.3 17.2 - - - -
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 4.9 0.2 - - - -
45A ASP* 1.3 102.4 + - - +
47A VAL* 1.3 69.5 + - - +
48A LYS* 6.2 1.3 - - - -
53A TRP* 3.0 76.2 + - + +
88B GLU 5.6 1.8 - - - -
89B LYS* 3.3 38.5 - - + +
93B PHE* 3.8 2.9 - - - -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 3.7 28.7 - - + -
46A ARG* 1.3 84.1 - - - +
48A LYS* 1.3 63.1 + - - +
51A TYR 3.4 8.3 - - - +
52A ALA* 3.9 8.7 - - + -
53A TRP* 4.2 2.5 - - - -
74A HIS* 3.3 41.3 - - + +
75A ALA* 3.6 10.9 - - - +
88B GLU 5.1 0.5 - - - +
89B LYS* 3.1 14.6 + - - +
90B GLY* 3.8 10.8 + - - -
92B SER 4.3 3.1 - - - +
93B PHE* 4.0 19.1 - - + -
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ARG* 6.2 1.3 - - - -
47A VAL* 1.3 76.8 - - - +
49A ASP* 1.3 101.4 + - - +
51A TYR* 2.9 27.5 + - + +
53A TRP* 3.6 20.3 - - + -
74A HIS* 3.5 4.0 - - - -
75A ALA* 4.5 19.3 + - + -
77A PRO* 5.1 7.9 - - - +
88B GLU 5.7 2.2 - - - +
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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