Contacts of the strand formed by residues 95 - 99 (chain A) in PDB entry 5FOR
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.6 9.4 - - + +
66A VAL* 3.9 17.0 - - + -
88A ALA 5.2 0.2 - - - +
89A PHE* 3.6 32.1 - - + +
90A HIS 3.8 1.6 - - - +
91A PRO 3.5 17.7 - - - +
92A PRO* 3.2 11.5 + - + +
93A HIS 3.4 2.2 - - - +
94A ARG* 1.3 80.8 - - + +
96A VAL* 1.3 69.5 + - - +
118A TRP* 3.5 44.7 - - + +
119A GLN* 3.4 22.9 + - - +
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Residues in contact with VAL 96 (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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63A CYS* 4.8 3.8 - - - -
64A VAL 2.9 13.4 + - - +
65A VAL* 3.3 17.3 - - + -
66A VAL* 2.6 35.7 + - - +
95A VAL* 1.3 81.9 - - - +
97A ARG* 1.3 58.8 + - - +
119A GLN* 3.4 28.3 - - + +
121A LEU* 3.6 33.4 - - + -
133A ALA* 4.2 11.0 - - + +
134A VAL* 4.8 3.4 - - + +
137A ALA* 4.1 23.6 - - + -
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Residues in contact with ARG 97 (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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65A VAL* 5.6 0.2 - - - -
66A VAL* 3.3 12.8 - - + +
68A LEU* 4.3 5.4 - - + -
96A VAL* 1.3 77.9 - - - +
98A LEU* 1.3 55.4 + - - +
99A LEU* 4.3 10.9 - - + +
104A ASP* 3.6 6.1 + - - -
115A TRP* 2.7 82.2 + - + +
116A ALA* 4.8 4.2 + - - +
118A TRP* 3.4 34.3 + - + +
119A GLN 2.9 14.4 + - - +
120A GLU* 2.7 44.6 + - + +
121A LEU* 2.7 35.3 + - - +
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Residues in contact with LEU 98 (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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20A TRP* 3.6 43.7 - - + -
24A LEU* 4.6 7.6 - - + -
65A VAL* 5.3 3.3 - - + +
66A VAL 2.8 9.3 + - - +
67A LEU* 3.6 26.3 - - + -
68A LEU* 2.7 33.7 + - - +
97A ARG* 1.3 73.8 - - - +
99A LEU* 1.3 66.7 + - - +
100A CYS* 3.2 6.2 + - + -
121A LEU* 3.4 31.6 - - + +
122A THR 3.5 25.4 - - - +
123A CYS 4.1 1.1 - - - +
130A TYR* 4.1 9.0 - - + +
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Residues in contact with LEU 99 (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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68A LEU* 3.5 31.0 - - + -
97A ARG* 4.3 7.0 - - - -
98A LEU* 1.3 69.2 - - - +
100A CYS* 1.3 60.0 + - - +
101A GLY 3.7 2.9 + - - -
102A VAL 3.7 20.6 - - - +
103A ARG* 5.3 0.7 - - - -
104A ASP* 4.3 15.7 - - + +
120A GLU* 3.5 39.9 - - + +
121A LEU 2.9 20.1 + - - +
122A THR* 4.7 12.8 - - + -
123A CYS* 3.3 24.4 + - - -
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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