Contacts of the strand formed by residues 96 - 102 (chain A) in PDB entry 6FIT
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 HIS 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A PHE* 3.1 19.9 - + + -
37A LEU* 4.8 7.0 - - + -
38A VAL 3.4 5.8 - - - +
39A CYS* 3.8 14.6 - - + +
81A SER 4.2 0.3 - - - +
82A MET* 3.9 21.8 - - - +
83A GLN 4.6 6.4 + - - +
90A GLN* 4.3 3.6 - - + +
92A VAL* 3.5 25.6 - - + -
94A HIS 2.6 21.9 + - - -
95A VAL* 1.3 77.0 - - - +
97A VAL* 1.4 61.0 + - - +
98A HIS* 3.7 16.4 + + - -
148A AMW 2.5 52.6 + - - -
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Residues in contact with VAL 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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37A LEU* 3.2 6.9 - - - -
38A VAL* 2.7 38.4 + - + +
58A LEU* 3.8 17.9 - - + -
59A PHE* 3.8 29.6 - - + -
62A THR* 3.5 39.0 - - + +
80A PHE* 4.4 6.7 - - + -
81A SER 4.1 12.3 - - - +
82A MET* 4.9 4.7 - - + -
96A HIS* 1.4 71.3 - - - +
98A HIS* 1.3 75.0 + - - +
99A VAL* 3.7 1.2 + - - +
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Residues in contact with HIS 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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35A HIS* 4.1 14.1 + + - +
36A VAL 3.9 2.7 - - - -
37A LEU* 3.9 18.1 - - + +
79A THR 3.6 1.5 - - - +
80A PHE* 3.3 8.1 - - - -
81A SER* 3.0 46.4 + - - +
83A GLN* 4.2 13.1 + - + -
96A HIS* 3.7 19.7 - + - -
97A VAL* 1.3 76.3 - - - +
99A VAL* 1.3 61.6 + - - +
100A LEU* 4.2 14.5 - - + +
148A AMW 2.9 52.1 + - - -
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Residues in contact with VAL 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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34A GLY 3.4 2.3 - - - +
35A HIS* 3.3 6.6 - - - -
36A VAL* 2.9 47.9 + - + +
38A VAL* 4.1 26.0 - - + -
62A THR* 4.3 5.8 - - + +
65A VAL* 4.5 3.6 - - + -
66A GLY* 3.9 15.0 - - - -
69A VAL* 4.0 9.2 - - + -
78A LEU* 3.6 25.6 - - + -
79A THR 3.7 2.2 - - - +
80A PHE* 4.2 18.8 - - + -
97A VAL 4.2 1.3 - - - +
98A HIS* 1.3 77.5 - - - +
100A LEU* 1.3 65.6 + - - +
101A PRO 4.2 0.2 - - - -
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Residues in contact with LEU 100 (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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31A VAL* 4.5 13.2 - - + -
32A VAL* 3.7 19.7 - - + -
35A HIS* 3.3 34.8 - - + +
78A LEU* 3.3 6.2 - - - -
79A THR* 2.9 53.0 + - + +
81A SER* 5.9 2.0 - - - -
98A HIS* 4.2 13.5 - - + +
99A VAL* 1.3 77.9 - - - +
101A PRO* 1.3 66.5 - - - +
102A ARG* 3.3 23.5 + - - +
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Residues in contact with PRO 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A VAL* 4.0 12.1 - - + +
33A PRO* 3.6 16.2 - - - +
34A GLY* 3.1 33.0 - - - +
35A HIS 4.1 0.7 - - - +
69A VAL* 3.3 39.9 - - + +
70A GLU* 4.3 4.9 - - - -
73A PHE* 4.3 8.1 - - + +
75A GLY* 4.5 8.3 - - - -
77A SER 3.7 5.6 - - - +
78A LEU* 3.8 5.4 - - + -
99A VAL 3.9 0.9 - - - +
100A LEU* 1.3 83.7 - - + +
102A ARG* 1.3 63.7 + - - +
103A LYS* 4.3 0.5 + - - +
106A ASP* 4.6 1.2 - - - +
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Residues in contact with ARG 102 (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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32A VAL* 4.9 5.8 - - - +
75A GLY* 3.8 1.9 - - - -
76A THR* 2.6 37.4 + - - -
77A SER* 2.6 29.7 + - - +
78A LEU 4.2 1.6 - - - -
79A THR* 3.2 27.5 + - - +
100A LEU* 3.4 36.8 - - - +
101A PRO* 1.3 80.6 - - - +
103A LYS* 1.3 55.7 + - - +
106A ASP* 3.0 34.2 + - - +
107A PHE* 3.4 20.6 + - - +
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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