Contacts of the strand formed by residues 3 - 15 (chain B) 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 PHE 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.5 38.6 - - + -
3A PHE* 3.8 21.1 - + + -
1B MET* 3.4 39.4 + - + -
2B ASP* 1.3 78.2 - - - +
4B ARG* 1.3 69.4 + - - +
94B ARG* 3.8 23.8 - - + -
155B LEU* 4.1 19.5 - - + -
156B VAL 3.2 16.6 - - - -
157B VAL* 3.8 12.8 - - + -
3C PHE* 4.0 16.4 - + + -
94C ARG* 4.3 10.0 - - - +
155C LEU* 3.1 27.4 - - + +
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Residues in contact with ARG 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ASP* 2.9 40.0 + - - +
3B PHE* 1.3 84.6 - - - +
5B ILE* 1.3 64.0 + - - +
53B ALA 3.2 24.0 + - - +
55B ALA* 5.2 1.0 - - - +
91B PHE* 3.6 41.3 - - + -
154B ALA 3.8 0.2 - - - +
155B LEU* 3.4 5.8 - - - +
156B VAL* 2.8 39.9 + - + +
158B ARG* 4.6 7.7 - - - +
95C ASN* 3.3 25.3 - - - +
127C ASP* 3.2 36.2 + - - +
128C ARG* 3.4 26.5 - - - +
155C LEU* 3.9 0.9 - - - -
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Residues in contact with ILE 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 4.2 16.2 - - + -
4B ARG* 1.3 77.0 - - - +
6B GLY* 1.3 59.7 + - - +
53B ALA* 3.5 8.3 - - - -
154B ALA 3.3 4.7 - - - +
155B LEU* 3.7 19.5 - - + -
5C ILE* 3.8 27.8 - - + -
6C GLY 4.5 1.1 - - - +
95C ASN* 2.8 38.7 + - - +
97C ASP* 3.8 5.4 - - - +
153C ALA* 3.6 17.3 - - + -
154C ALA 3.2 44.6 - - - +
155C LEU* 3.5 8.3 - - + +
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Residues in contact with GLY 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 4.5 1.9 - - - +
5B ILE* 1.3 74.0 - - - +
7B GLN* 1.3 60.5 + - - +
49B ALA* 3.3 23.8 - - - -
53B ALA* 3.4 6.7 - - - +
153B ALA* 3.4 5.2 - - - +
154B ALA 2.9 31.7 + - - +
97C ASP* 3.4 11.0 - - - -
153C ALA* 4.8 3.7 - - - +
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Residues in contact with GLN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLY* 1.3 73.9 - - - +
8B GLY* 1.3 61.4 + - - +
49B ALA* 3.5 8.3 - - - +
152B ALA 3.2 11.7 - - - +
153B ALA* 5.0 2.5 - - + -
97C ASP* 2.9 12.0 + - - +
98C SER 3.3 10.2 - - - -
99C THR* 2.7 24.7 + - - -
132C LYS* 2.7 42.3 + - - -
151C GLN* 2.9 40.6 + - - +
152C ALA 4.5 1.6 - - - -
153C ALA* 3.9 30.5 - - + +
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Residues in contact with GLY 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLN* 1.3 82.9 + - - +
9B TYR* 1.3 61.3 + - - +
45B ALA* 3.3 24.7 - - - -
48B ASP* 4.1 5.2 - - - -
49B ALA* 3.7 4.0 - - - +
151B GLN* 3.5 5.4 - - - +
152B ALA 2.9 32.1 + - - +
99C THR* 4.8 0.2 - - - -
132C LYS* 4.6 1.6 - - - -
151C GLN* 4.6 0.3 - - - +
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Residues in contact with TYR 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLY* 1.3 76.1 - - - +
10B ASP* 1.3 70.9 + - - +
11B VAL* 3.6 23.3 - - + +
44B HIS 5.3 0.3 - - - -
45B ALA* 4.1 6.1 - - - +
48B ASP* 4.2 6.2 + - - +
141B TYR* 4.0 7.6 + - - -
149B GLU* 3.4 37.0 + - + -
150B ALA 3.6 8.5 - - - -
151B GLN* 5.0 3.8 - - + -
99C THR* 4.7 10.6 + - + -
101C ILE* 3.5 31.7 - - + +
134C LYS* 3.3 30.8 + - + +
135C THR 4.7 4.3 - - - -
136C ASN* 2.6 27.6 + - - -
142C LEU* 5.1 0.7 - - - +
149C GLU* 5.4 0.4 - - - -
151C GLN* 3.4 34.1 - - - +
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Residues in contact with ASP 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 1.3 83.0 - - - +
11B VAL* 1.3 75.0 + - - +
12B HIS* 3.3 6.9 - - - -
41B VAL* 3.3 24.6 - - - +
44B HIS* 3.1 18.4 + - + +
45B ALA* 4.1 2.2 - - + +
149B GLU* 3.4 7.1 - - - +
150B ALA 3.0 30.5 + - - +
164B ZN 2.3 32.4 - - - -
134C LYS* 2.6 29.5 + - - +
137C GLU* 5.6 1.0 - - - +
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Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 3.6 14.4 - - + +
10B ASP* 1.3 82.5 + - - +
12B HIS* 1.3 75.6 + - - +
41B VAL* 3.9 0.7 - - - -
141B TYR* 4.1 15.5 - - + +
148B ILE 3.3 20.2 - - - +
149B GLU* 4.4 4.9 - - + -
134C LYS* 5.0 0.9 - - - +
135C THR 4.4 2.7 - - - +
136C ASN* 3.5 44.6 - - - +
137C GLU* 3.1 23.0 - - + +
139C LEU* 3.8 21.1 - - + -
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Residues in contact with HIS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASP* 3.3 9.6 - - - -
11B VAL* 1.3 78.2 + - - +
13B GLN* 1.3 61.4 + - - +
33B LEU* 3.7 20.1 - - + +
34B LEU 2.7 26.8 + - - +
39B ALA* 3.7 23.7 - - + -
41B VAL* 3.4 16.5 - - + +
44B HIS* 3.8 2.5 + + - -
147B GLY* 3.2 2.4 - - - -
148B ILE 3.0 31.1 + - - -
164B ZN 1.9 37.6 - - - -
137C GLU* 4.0 25.2 - - - -
139C LEU* 4.1 5.7 - - - +
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Residues in contact with GLN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B HIS* 1.3 74.7 + - - +
14B LEU* 1.3 58.5 + - - +
15B VAL* 4.0 11.4 + - + +
32B GLY 3.5 0.7 - - - +
33B LEU* 3.2 7.8 - - - -
34B LEU* 3.2 51.6 + - + +
146B GLU 3.5 6.5 - - - +
147B GLY* 4.1 0.9 - - - -
137C GLU* 3.0 32.4 + - + +
138C LYS* 4.1 15.0 + - - +
139C LEU* 3.7 23.9 - - + +
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLN* 1.3 71.8 - - - +
15B VAL* 1.3 65.5 + - - +
20B LEU* 4.2 6.5 - - + -
29B TYR* 4.1 20.9 - - + +
31B ARG* 3.6 22.3 + - + +
32B GLY* 3.5 24.7 - - - +
33B LEU* 3.7 20.4 - - + -
104B ALA 4.4 6.5 - - - +
145B GLY* 3.3 39.5 - - - +
146B GLU* 2.8 13.7 + - - +
147B GLY* 3.8 12.1 - - - +
148B ILE* 4.0 23.3 - - + -
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Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLN* 4.4 16.8 - - - +
14B LEU* 1.3 80.2 - - - +
16B PRO* 1.4 84.3 - - + +
17B GLY 3.5 0.7 + - - -
18B ARG* 4.1 2.2 + - + +
31B ARG* 3.8 6.7 - - - +
32B GLY* 2.9 26.0 + - - +
34B LEU* 3.7 37.7 - - + -
146B GLU 5.4 0.9 - - - +
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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