Contacts of the helix formed by residues 92 - 101 (chain A) in PDB entry 4FWF
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 CYS 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A CYS* 3.2 10.8 - - - -
72A ARG 4.5 3.1 - - - -
73A CYS* 4.5 1.6 - - - -
74A ALA* 4.6 8.3 - - + +
79A THR* 4.3 14.6 - - - -
81A ARG 3.9 5.6 - - - -
82A TRP* 3.5 17.6 - - + -
83A TYR* 4.0 0.8 - - - -
91A PHE* 1.3 78.1 - - - +
93A ASN* 1.3 58.8 + - - +
94A GLU* 3.2 15.7 - - - +
95A CYS* 3.0 21.8 - - - -
96A PHE* 3.2 22.9 + - - +
902A ZN 2.3 33.4 - - - -
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Residues in contact with ASN 93 (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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79A THR* 4.4 3.5 - - - -
80A SER* 3.5 28.0 + - - +
81A ARG* 3.4 16.4 + - - +
83A TYR* 2.7 39.0 + - - -
92A CYS* 1.3 72.8 - - - +
94A GLU* 1.3 60.2 + - - +
96A PHE* 3.7 11.0 - - - -
97A ASP* 2.9 55.3 + - - +
101A ARG* 4.9 3.0 + - - +
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Residues in contact with GLU 94 (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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70A SER* 4.2 9.6 + - - +
72A ARG* 2.8 42.6 - - + +
92A CYS* 3.2 7.7 - - - -
93A ASN* 1.3 78.4 - - - +
95A CYS* 1.3 51.6 + - - +
97A ASP* 3.1 9.7 + - - +
98A HIS* 2.8 32.7 + - - +
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Residues in contact with CYS 95 (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 CYS* 4.0 4.0 - - - -
67A ALA* 4.3 10.5 - - + -
68A SER 4.1 1.3 - - - -
69A ALA* 3.6 31.9 - - + -
70A SER* 3.7 9.2 - - - -
73A CYS* 3.6 8.5 - - - -
91A PHE* 4.8 5.8 - - + -
92A CYS* 3.0 10.1 - - - +
94A GLU* 1.3 73.3 - - - +
96A PHE* 1.3 64.9 + - - +
98A HIS* 3.1 21.7 - - - +
99A TYR* 3.3 18.2 - - + -
131A MET* 5.1 0.8 - - - +
902A ZN 2.2 36.3 - - - -
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Residues in contact with PHE 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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83A TYR* 3.9 33.4 - + + -
91A PHE* 3.7 28.1 - + + -
92A CYS 3.2 19.8 + - - +
93A ASN* 3.6 15.0 - - - +
94A GLU 3.2 0.2 - - - -
95A CYS* 1.3 77.6 - - - +
97A ASP* 1.3 71.4 + - - +
99A TYR* 3.6 3.5 + - - +
100A TYR* 3.0 62.9 + + + +
101A ARG* 5.1 4.5 - - - -
127A PRO* 3.6 35.9 - - + +
128A LYS* 5.4 2.2 - - + -
131A MET* 6.0 0.2 - - - -
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Residues in contact with ASP 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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93A ASN* 2.9 41.2 + - - +
94A GLU* 3.4 7.6 - - - +
96A PHE* 1.3 82.6 - - - +
98A HIS* 1.3 67.4 + - - +
101A ARG* 2.9 73.7 + - + +
103A HIS* 6.2 0.9 - - + -
104A LYS* 3.6 10.7 - - + +
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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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69A ALA* 2.9 43.6 + - + -
70A SER* 3.5 13.9 - - - -
94A GLU 2.8 13.1 + - - +
95A CYS* 3.1 18.6 - - - +
97A ASP* 1.3 76.4 - - - +
99A TYR* 1.3 65.7 + + + +
104A LYS* 3.3 19.0 - - + +
105A ASP* 4.0 19.2 + - + +
106A GLY* 3.1 50.3 + - - -
107A TYR 3.3 4.2 + - - -
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Residues in contact with TYR 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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67A ALA* 5.6 1.0 - - + +
69A ALA* 3.3 29.6 - - + +
95A CYS 3.3 24.0 - - - -
96A PHE* 3.6 4.1 + - - +
97A ASP 3.1 0.2 - - - -
98A HIS* 1.3 81.2 - + - +
100A TYR* 1.3 66.5 + - - +
101A ARG 3.4 0.7 - - - -
106A GLY* 3.2 35.4 - - - -
107A TYR* 3.2 24.5 - - - -
109A LYS* 4.4 11.8 + - + -
110A TYR* 3.7 26.3 - - + +
127A PRO* 5.9 4.0 - - + -
130A PHE* 3.8 35.9 - + + -
131A MET* 4.0 20.0 - - + -
135A GLN* 3.4 23.1 + - + -
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Residues in contact with TYR 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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96A PHE* 3.0 48.4 + + + +
97A ASP* 4.6 0.4 - - - -
99A TYR* 1.3 78.9 - - - +
101A ARG* 1.3 80.4 + - - +
102A SER 4.0 0.3 + - - -
107A TYR* 3.5 17.0 - - - -
110A TYR* 4.6 16.4 - + - -
127A PRO* 3.7 29.4 - - + -
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Residues in contact with ARG 101 (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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93A ASN* 4.9 2.6 + - - +
96A PHE* 5.1 4.2 - - - -
97A ASP* 2.9 59.0 + - + +
99A TYR 3.4 0.2 - - - -
100A TYR* 1.3 100.7 - - + +
102A SER* 1.3 66.9 + - - +
103A HIS* 4.0 30.3 + - + +
104A LYS* 3.0 19.5 + - + +
107A TYR* 3.5 11.4 - - - +
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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