Contacts of the helix formed by residues 93 - 102 (chain A) in PDB entry 4F4I
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 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PHE* 3.6 29.9 - + - -
6A THR* 3.8 14.4 - - + +
8A GLU* 2.9 17.6 + - - +
37A GLU* 3.6 16.2 - - - -
70A ARG* 2.9 29.7 + - + +
74A LEU* 3.8 16.2 - - + +
78A VAL* 6.4 0.7 - - + -
90A CYS* 4.7 4.3 - - - -
92A ARG* 1.3 78.3 - - - +
94A ILE* 1.3 86.1 + - + +
95A ASP 3.1 3.2 + - - +
96A SER* 3.2 10.9 - - - -
97A SER 3.5 1.4 + - - -
120A ILE* 3.2 29.2 - - + +
123A LEU* 2.6 26.8 + - - +
124A TYR* 4.4 0.9 - - - -
125A PRO* 3.7 27.6 - - + -
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Residues in contact with ILE 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 ARG* 4.0 4.7 - - - +
93A TYR* 1.3 101.6 - - + +
95A ASP* 1.3 85.3 + - - +
97A SER* 3.4 10.4 + - - -
98A LEU* 3.4 34.5 + - + +
113A ARG* 4.9 10.3 - - + +
116A ASN* 3.5 30.5 + - + -
117A GLU* 5.0 3.4 - - + +
120A ILE* 4.1 23.1 - - + -
124A TYR* 4.5 14.1 - - + -
177A ARG* 4.2 11.0 - - - +
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Residues in contact with ASP 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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6A THR* 4.7 0.9 + - - -
8A GLU* 3.7 25.8 - - + +
93A TYR* 3.1 2.4 + - - +
94A ILE* 1.3 85.4 + - - +
96A SER* 1.3 64.8 + - - +
98A LEU* 3.3 8.3 + - - +
99A ALA* 3.1 21.5 + - - +
128A THR* 4.2 1.7 + - - +
167A TYR* 4.0 5.7 - - + -
170A ILE* 3.3 29.2 - - + +
177A ARG* 2.9 39.9 + - - -
178A PHE* 3.5 23.2 - - + -
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Residues in contact with SER 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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8A GLU* 3.1 19.8 + - - -
70A ARG* 4.8 2.5 - - - -
92A ARG* 3.2 46.1 + - - +
93A TYR 3.2 11.4 - - - -
95A ASP* 1.3 72.5 - - - +
97A SER* 1.3 65.5 + - - -
99A ALA 3.4 0.9 + - - -
100A TYR* 3.0 36.4 + - - +
167A TYR* 3.9 8.1 - - - -
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Residues in contact with SER 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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66A PHE* 5.6 0.6 - - - +
70A ARG* 2.8 35.3 + - - -
93A TYR 3.7 1.4 + - - -
94A ILE 3.4 5.1 + - - -
96A SER* 1.3 77.0 - - - +
98A LEU* 1.3 55.2 + - - +
100A TYR* 5.0 1.1 - - - -
101A GLN* 2.7 53.6 + - - +
102A GLY 3.2 1.7 + - - -
112A VAL* 3.6 4.8 - - - +
116A ASN* 3.3 26.4 + - - -
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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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94A ILE* 3.4 26.1 + - + +
95A ASP* 3.3 19.9 + - - +
96A SER 3.2 0.8 - - - -
97A SER* 1.3 79.1 - - - +
99A ALA* 1.3 57.6 + - - +
102A GLY* 2.8 24.6 + - - +
103A TYR* 2.9 12.1 + - - +
109A VAL* 3.1 49.5 - - + +
112A VAL* 4.1 6.3 - - + +
113A ARG* 3.7 43.1 - - + +
116A ASN* 5.6 0.4 - - - +
170A ILE* 3.6 19.1 - - + -
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Residues in contact with ALA 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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95A ASP 3.1 16.4 + - - +
96A SER 4.2 1.8 - - - +
98A LEU* 1.3 75.2 - - - +
100A TYR* 1.3 60.2 + - + +
103A TYR* 3.7 4.9 - - - +
104A ALA* 2.8 31.1 + - - +
162A LYS 4.8 0.2 - - - +
163A VAL* 3.7 28.0 - - + +
166A GLY 4.0 7.0 - - - -
167A TYR* 3.8 31.4 - - + +
170A ILE* 3.8 4.2 - - + +
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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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10A PRO* 4.1 0.2 - - - +
11A GLU* 3.9 13.3 + - - +
92A ARG* 3.2 43.4 + - - -
96A SER* 3.0 33.0 + - - +
97A SER* 4.5 1.6 - - - +
99A ALA* 1.3 77.5 - - + +
101A GLN* 1.3 68.9 + - + +
104A ALA* 3.3 6.9 - - - +
105A ARG* 2.8 34.3 + - + +
159A PHE* 3.8 20.5 - + + -
163A VAL* 3.5 42.1 - - + +
167A TYR* 4.2 4.5 - - - -
173B ASN* 5.6 1.9 + - - -
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Residues in contact with GLN 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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59A ILE* 5.2 2.2 + - + +
62A GLU* 5.4 1.0 + - - +
63A ALA* 4.0 16.3 - - + +
66A PHE* 3.1 46.4 - - - +
97A SER* 2.7 37.6 + - - +
100A TYR* 1.3 82.5 - - - +
102A GLY* 1.3 62.5 + - - +
103A TYR 3.5 0.2 - - - -
105A ARG* 3.8 26.4 - - + +
106A GLY 3.9 0.2 + - - -
107A ILE* 3.3 41.8 + - + +
112A VAL* 3.9 10.2 - - + +
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Residues in contact with GLY 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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97A SER 3.2 5.1 + - - -
98A LEU 2.8 17.0 + - - -
101A GLN* 1.3 73.1 - - - +
103A TYR* 1.3 57.0 + - - +
106A GLY* 3.8 2.3 - - - -
107A ILE 3.4 4.9 + - - -
108A GLY* 2.8 37.2 + - - -
109A VAL* 3.8 8.6 + - - -
112A VAL* 3.5 21.7 - - - +
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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