Contacts of the strand formed by residues 147 - 157 (chain A) in PDB entry 3IEQ
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 GLY 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A VAL* 4.9 0.2 - - - -
12A HIS 3.1 14.8 - - - -
13A GLN* 4.1 0.9 - - - -
14A LEU* 3.7 8.0 - - - +
101A ILE 4.6 1.0 - - - +
102A ALA* 5.2 1.7 - - - -
103A GLN 5.6 0.5 + - - -
141A TYR* 3.9 4.2 + - - -
142A LEU* 3.2 26.8 - - - +
145A GLY* 3.4 4.1 - - - -
146A GLU* 1.3 79.9 + - - +
148A ILE* 1.3 66.3 - - - +
139B LEU* 4.2 10.0 - - - +
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Residues in contact with ILE 148 (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* 3.4 5.9 - - - +
12A HIS* 3.1 28.7 + - - +
14A LEU* 4.1 14.6 - - + -
20A LEU* 4.4 7.6 - - + -
22A ILE* 3.9 21.5 - - + -
33A LEU* 3.8 22.2 - - + -
41A VAL* 3.6 17.9 - - + +
100A ILE* 3.7 22.9 - - + -
101A ILE 3.5 13.2 - - - +
102A ALA* 3.7 21.1 - - + -
104A ALA 3.9 12.1 - - - +
105A PRO* 4.8 3.6 - - + -
107A LEU* 5.7 0.2 - - + -
142A LEU* 4.0 0.4 - - - -
147A GLY* 1.3 78.8 - - - +
149A GLU* 1.3 63.5 + - - +
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Residues in contact with GLU 149 (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 TYR* 3.5 30.3 + - + -
10A ASP 3.3 12.6 - - - +
11A VAL* 4.2 5.4 - - + +
41A VAL* 4.0 1.8 - - - -
100A ILE* 3.4 4.0 - - - +
101A ILE* 2.8 43.5 + - + +
141A TYR* 4.5 5.0 + - - -
142A LEU* 3.5 29.9 - - + +
148A ILE* 1.3 78.4 - - - +
150A ALA* 1.3 67.2 + - - +
151A GLN* 2.8 34.1 + - - +
9C TYR* 5.2 4.5 + - - -
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Residues in contact with ALA 150 (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 TYR* 3.6 3.6 - - - -
10A ASP 2.8 32.1 + - - +
41A VAL* 3.6 30.0 - - + +
42A LEU* 3.7 22.7 - - + +
45A ALA* 3.8 5.1 - - + +
99A THR 3.1 11.7 - - - +
100A ILE* 4.6 2.0 - - - -
101A ILE* 4.7 0.2 - - - -
149A GLU* 1.3 75.8 - - - +
151A GLN* 1.3 67.5 + - - +
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Residues in contact with GLN 151 (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 GLY 3.4 9.6 - - - +
9A TYR* 5.0 5.4 - - + -
45A ALA* 4.3 1.5 - - - +
98A SER* 3.1 7.2 - - - -
99A THR* 2.8 32.7 + - - +
101A ILE* 3.6 11.7 - - + +
149A GLU* 2.8 25.8 + - - +
150A ALA* 1.3 80.0 - - - +
152A ALA* 1.3 61.4 + - - +
7C GLN* 2.9 29.9 + - - +
8C GLY 4.9 0.2 - - - +
9C TYR* 3.3 43.7 - - - +
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Residues in contact with ALA 152 (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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7A GLN* 3.3 5.9 - - - +
8A GLY 2.8 30.8 + - - +
45A ALA* 3.5 32.1 - - + +
46A ILE* 3.7 22.7 - - + +
49A ALA* 4.0 4.0 - - + -
96A VAL* 5.3 0.7 - - + -
97A ASP 3.3 8.7 - - - +
98A SER* 4.1 0.4 - - - +
151A GLN* 1.3 77.2 - - - +
153A ALA* 1.3 62.6 + - - +
7C GLN* 4.4 4.8 - - - +
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Residues in contact with ALA 153 (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 GLY 3.4 7.9 - - - +
7A GLN* 5.1 2.9 - - + -
49A ALA* 4.3 2.5 - - - -
96A VAL* 3.4 5.1 - - - +
97A ASP* 2.8 34.0 + - + +
152A ALA* 1.3 76.0 - - - +
154A ALA* 1.3 60.8 + - - +
5C ILE* 3.6 22.3 - - + +
6C GLY 4.9 1.8 - - - +
7C GLN* 3.9 27.1 - - + +
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Residues in contact with ALA 154 (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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4A ARG 4.0 0.3 - - - +
5A ILE* 3.4 2.3 - - - -
6A GLY 3.0 30.3 + - - +
46A ILE* 6.1 0.2 - - + -
49A ALA* 4.1 21.7 - - + +
50A LEU* 3.8 30.1 - - + -
53A ALA* 4.3 3.2 - - + +
95A ASN 3.4 10.1 - - - +
96A VAL* 4.2 4.9 - - + -
153A ALA* 1.3 76.0 - - - +
155A LEU* 1.3 61.2 + - - +
5C ILE* 3.3 10.8 - - - +
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Residues in contact with LEU 155 (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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3A PHE* 4.0 29.6 - - + -
4A ARG 3.5 17.0 - - - +
5A ILE* 3.6 19.3 - - + -
93A ILE* 3.9 1.0 - - - +
94A ARG* 2.8 36.3 + - + -
95A ASN* 3.0 23.7 + - - +
154A ALA* 1.3 73.6 - - - +
156A VAL* 1.3 58.6 + - - +
155B LEU* 4.9 4.5 - - + -
3C PHE* 3.2 46.7 - - + +
4C ARG* 3.9 6.5 - - - +
5C ILE* 3.8 13.1 - - + +
155C LEU* 5.1 2.2 - - + -
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Residues in contact with VAL 156 (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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3A PHE* 3.3 12.7 - - - -
4A ARG* 2.9 44.6 + - + +
50A LEU* 4.4 13.7 - - + +
53A ALA* 3.8 26.2 - - + +
54A ALA* 4.8 0.7 - - + +
86A VAL* 4.6 9.2 - - + -
91A PHE* 3.7 27.6 - - + -
92A ALA 3.3 15.9 - - - +
93A ILE* 4.1 18.2 - - + -
94A ARG* 4.1 2.5 - - - +
154A ALA* 5.1 0.2 - - + -
155A LEU* 1.3 78.1 - - - +
157A VAL* 1.3 62.3 + - - +
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Residues in contact with VAL 157 (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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1A MET 4.4 6.7 - - - +
2A ASP 3.4 28.7 - - - +
3A PHE* 3.8 22.7 - - + -
90A GLY 4.0 0.5 - - - +
91A PHE* 3.4 5.1 - - - -
92A ALA* 3.0 42.7 + - + +
94A ARG* 3.4 38.6 - - + +
156A VAL* 1.3 77.5 - - - +
158A ARG* 1.3 70.4 + - - +
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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