Contacts of the strand formed by residues 125 - 134 (chain A) in PDB entry 4ICX
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 GLU 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLY* 3.2 3.1 - - - -
18A ARG* 2.7 75.5 + - + -
19A HIS* 4.6 4.0 - - - -
20A PHE* 3.5 2.5 - - - -
111A TRP* 3.6 23.7 - - + +
112A TYR 3.2 19.7 - - - +
113A GLN* 3.7 19.7 + - - +
114A LEU* 4.5 1.3 - - - +
123A LYS* 3.8 10.0 - - - +
124A SER* 1.3 76.9 - - - +
126A ILE* 1.3 65.5 + - - +
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Residues in contact with ILE 126 (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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14A ILE* 3.6 28.5 - - + -
16A GLU 3.6 9.9 - - - +
20A PHE* 4.0 12.3 - - + -
30A VAL* 4.1 19.7 - - + -
52A PHE* 4.1 23.3 - - + -
77A LEU* 6.0 0.7 - - + -
79A CYS* 4.4 5.8 - - + -
95A ILE* 3.9 15.3 - - + -
111A TRP* 3.7 3.8 - - - -
112A TYR* 3.0 31.6 + - - +
114A LEU* 3.7 25.6 - - + -
125A GLU* 1.3 78.3 - - - +
127A GLN* 1.3 67.7 + - - +
128A ILE* 3.7 10.1 + - + +
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Residues in contact with GLN 127 (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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14A ILE* 3.9 0.3 - - - -
15A LEU* 3.0 41.7 + - + +
16A GLU* 2.8 26.4 + - - +
109A PRO* 3.6 34.0 + - + +
110A LYS 3.4 11.9 - - - +
111A TRP* 3.6 43.1 - - + +
126A ILE* 1.3 72.5 - - - +
128A ILE* 1.3 64.6 + - - +
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Residues in contact with ILE 128 (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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12A VAL* 4.0 5.6 - - + -
13A SER 3.3 9.6 - - - +
14A ILE* 4.5 5.8 - - + -
77A LEU* 3.7 27.1 - - + -
95A ILE* 4.2 20.6 - - + -
97A LEU* 3.9 26.7 - - + -
108A ALA 4.9 0.2 - - - +
109A PRO* 3.3 4.8 - - - +
110A LYS* 2.9 35.9 + - - +
112A TYR* 3.8 22.9 + - + -
126A ILE* 3.9 20.4 - - + +
127A GLN* 1.3 81.6 - - - +
129A SER* 1.3 74.6 + - - +
130A ILE* 5.4 1.3 - - + -
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Residues in contact with SER 129 (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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11A VAL 4.5 0.4 - - - -
12A VAL* 3.5 2.6 - - - -
13A SER* 2.9 45.4 + - - -
15A LEU* 4.1 3.7 - - - +
107A GLN* 3.4 20.9 + - - -
108A ALA 5.3 0.7 - - - -
109A PRO* 3.3 24.7 - - - +
128A ILE* 1.3 81.8 - - - +
130A ILE* 1.3 64.2 + - - +
131A ALA* 6.0 2.0 - - - -
71B GLN* 4.2 11.3 + - - -
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Residues in contact with ILE 130 (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 ILE* 4.1 7.6 - - + -
11A VAL 3.5 9.0 - - - +
12A VAL* 4.3 8.5 - - + -
75A ILE* 3.6 30.5 - - + -
97A LEU* 5.2 13.0 - - + -
98A ASP 4.2 13.9 - - - +
99A LEU* 3.8 18.2 - - + -
101A THR* 3.7 23.3 - - - +
102A ALA* 3.9 20.4 - - + +
103A GLN 4.9 0.9 + - - -
105A THR 4.9 0.7 - - - +
107A GLN* 4.8 17.0 + - - +
112A TYR* 5.4 6.7 - - - +
128A ILE* 5.7 1.6 - - + -
129A SER* 1.3 76.8 - - - +
131A ALA* 1.3 66.9 + - - +
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Residues in contact with ALA 131 (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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9A LEU 3.7 0.3 - - - +
10A ILE* 3.7 3.6 - - - -
11A VAL* 2.8 42.1 + - + +
102A ALA* 4.7 1.8 - - - -
103A GLN 3.7 5.4 - - - -
105A THR 3.8 20.4 - - - +
106A LYS* 4.4 15.3 - - + -
107A GLN 5.1 0.7 - - - +
129A SER* 6.0 2.2 - - - -
130A ILE* 1.3 79.6 - - - +
132A LEU* 1.3 67.7 + - - +
133A GLU* 5.7 4.9 - - + +
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Residues in contact with LEU 132 (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 LEU* 4.7 7.9 - - + -
9A LEU 3.3 6.1 - - - +
10A ILE* 3.8 27.6 - - + -
60A ILE* 5.6 0.7 - - + -
65A LEU* 3.5 38.6 - - + -
99A LEU* 4.7 0.2 - - + -
102A ALA* 3.5 33.0 - - + +
103A GLN 2.8 21.4 + - - +
104A GLU* 3.4 42.0 - - + +
105A THR 5.5 0.2 - - - -
131A ALA* 1.3 82.1 - - - +
133A GLU* 1.3 65.4 - - - +
55C GLU* 6.1 0.2 - - - +
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Residues in contact with GLU 133 (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 LEU* 3.3 10.7 - - - +
9A LEU* 2.7 49.7 + - + +
11A VAL* 4.1 26.6 - - + +
55A GLU* 5.3 3.8 - - - +
104A GLU* 5.6 0.4 - - - -
106A LYS* 4.0 24.3 + - + -
131A ALA* 5.6 4.8 - - + +
132A LEU* 1.3 79.5 - - - +
134A THR* 1.3 65.8 + - - +
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Residues in contact with THR 134 (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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5A SER* 4.9 10.1 - - - +
7A GLN 4.0 4.5 - - - -
8A LEU* 4.2 9.6 - - + -
9A LEU* 4.8 3.7 - - - +
62A ARG* 5.0 5.6 - - - +
104A GLU* 5.2 4.7 - - + +
133A GLU* 1.3 78.9 - - - +
135A ASP* 1.3 62.5 + - - +
53C ALA* 4.7 17.0 - - + +
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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