Contacts of the strand formed by residues 3 - 16 (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 PHE 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.2 43.9 + - - -
2A ASP* 1.3 77.7 + - - +
4A ARG* 1.3 70.5 + - - +
94A ARG* 3.6 29.8 - - + -
155A LEU* 4.0 24.9 - - + -
156A VAL 3.3 14.4 - - - +
157A VAL* 3.8 14.1 - - + -
3B PHE* 3.8 20.6 - + + -
94B ARG* 4.3 9.8 - - - +
155B LEU* 3.3 26.9 - - + +
1C MET 3.5 22.0 - - - -
3C PHE* 4.0 17.0 - + + -
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Residues in contact with ARG 4 (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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2A ASP* 3.0 38.7 + - - +
3A PHE* 1.3 85.5 - - - +
5A ILE* 1.3 65.2 + - - +
53A ALA* 3.2 26.0 + - - +
54A ALA 5.3 0.6 + - - -
55A ALA* 5.4 0.2 - - - +
91A PHE* 3.8 37.3 - - + -
154A ALA 4.0 0.2 - - - +
155A LEU* 3.5 4.8 - - - +
156A VAL* 2.9 38.5 + - + +
158A ARG* 4.4 6.9 - - - +
95B ASN* 3.4 26.0 - - - +
127B ASP* 3.3 33.7 + - - -
128B ARG* 3.4 29.0 - - - +
155B LEU* 4.1 0.9 - - - -
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Residues in contact with ILE 5 (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* 1.3 72.8 - - - +
6A GLY* 1.3 59.2 + - - +
53A ALA* 3.5 8.5 - - - -
154A ALA 3.4 5.6 - - - +
155A LEU* 3.6 24.9 - - + -
5B ILE* 4.2 22.4 - - + -
6B GLY 4.5 2.2 - - - +
95B ASN* 2.8 36.8 + - - +
97B ASP* 3.7 5.5 - - - +
153B ALA* 3.5 20.0 - - + -
154B ALA 3.5 39.7 - - - +
155B LEU* 4.1 15.0 - - + +
5C ILE* 4.2 14.1 - - + -
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Residues in contact with GLY 6 (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 ILE* 1.3 76.3 - - - +
7A GLN* 1.3 61.8 + - - +
49A ALA* 3.3 24.2 - - - -
53A ALA* 3.5 4.9 - - - +
153A ALA* 3.4 4.9 - - - +
154A ALA 3.0 29.9 + - - +
97B ASP* 3.3 11.9 - - - -
153B ALA* 4.9 3.3 - - - +
5C ILE* 4.5 1.6 - - - +
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Residues in contact with GLN 7 (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* 1.3 75.0 - - - +
8A GLY* 1.3 62.7 + - - +
49A ALA* 3.6 6.9 - - - +
152A ALA 3.3 10.1 - - - +
153A ALA* 5.1 2.7 - - + -
97B ASP* 3.0 11.6 + - - +
98B SER 3.2 11.4 - - - -
99B THR* 2.6 24.5 + - - -
132B LYS* 2.8 39.8 + - - -
151B GLN* 2.9 42.0 + - - +
152B ALA 4.5 1.8 - - - +
153B ALA* 3.8 31.6 - - + +
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Residues in contact with GLY 8 (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* 1.3 83.2 + - - +
9A TYR* 1.3 61.5 + - - +
45A ALA* 3.4 22.4 - - - -
48A ASP* 4.1 5.4 - - - -
49A ALA* 3.7 4.6 - - - +
151A GLN* 3.4 6.6 - - - +
152A ALA 2.8 30.6 + - - +
99B THR* 4.8 0.2 - - - -
132B LYS* 4.6 1.8 - - - -
151B GLN* 4.7 0.9 - - - +
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Residues in contact with TYR 9 (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* 1.3 74.9 - - - +
10A ASP* 1.3 71.0 + - - +
11A VAL* 3.4 24.5 - - + +
44A HIS 5.3 0.2 - - - +
45A ALA* 4.2 5.3 - - - +
48A ASP* 4.1 6.7 + - - +
141A TYR* 3.9 9.2 + - - -
149A GLU* 3.5 32.0 + - + -
150A ALA 3.6 9.9 - - - -
151A GLN* 5.0 4.9 - - + -
99B THR* 4.6 10.9 + - + +
101B ILE* 3.5 30.4 - - + +
134B LYS* 3.3 30.1 - - + +
135B THR 4.7 4.9 - - - -
136B ASN* 2.5 31.3 + - - -
142B LEU* 5.2 1.0 - - - +
149B GLU* 5.5 0.2 - - - -
151B GLN* 3.4 32.5 - - - +
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Residues in contact with ASP 10 (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* 1.3 81.7 - - - +
11A VAL* 1.3 69.5 + - - +
12A HIS* 3.1 9.2 + - - -
41A VAL* 3.4 22.6 - - - +
44A HIS* 3.0 13.7 + - + +
45A ALA* 4.0 8.0 - - + +
149A GLU* 3.3 5.9 - - - +
150A ALA 2.8 33.5 + - - +
163A ZN 2.1 37.0 - - - -
134B LYS* 2.9 27.7 + - - +
137B GLU* 5.7 0.2 - - - +
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Residues in contact with VAL 11 (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* 3.4 26.9 - - + +
10A ASP* 1.3 81.2 + - - +
12A HIS* 1.3 75.2 + - - +
41A VAL* 3.8 0.7 - - - -
141A TYR* 4.3 14.1 - - + -
148A ILE 3.4 20.6 - - - +
149A GLU* 4.3 5.8 - - + -
134B LYS* 4.6 0.9 + - - +
135B THR 4.5 2.0 - - - +
136B ASN* 3.4 34.5 - - - +
137B GLU* 3.2 15.3 - - + +
139B LEU* 3.7 22.0 - - + -
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Residues in contact with HIS 12 (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 ASP* 3.3 10.0 + - - -
11A VAL* 1.3 82.4 + - - +
13A GLN* 1.3 61.6 + - - +
33A LEU* 3.7 21.9 - - + +
34A LEU 2.8 25.6 + - - +
35A GLY* 4.2 7.9 - - - -
36A HIS 5.5 0.2 - - - -
39A ALA* 3.7 28.4 + - + +
41A VAL* 4.0 7.2 - - + -
44A HIS* 3.5 5.2 + + - -
147A GLY* 3.1 3.3 - - - -
148A ILE 3.1 31.9 + - - -
163A ZN 2.1 36.5 - - - -
137B GLU* 4.2 18.8 - - - -
139B LEU* 4.2 4.9 - - - -
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Residues in contact with GLN 13 (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 HIS* 1.3 76.1 - - - +
14A LEU* 1.3 59.2 + - - +
15A VAL* 4.2 16.1 - - + +
33A LEU* 3.3 3.2 - - - -
34A LEU* 2.9 53.9 + - + +
146A GLU 3.4 8.5 - - - +
147A GLY* 4.1 0.7 - - - -
137B GLU* 2.7 36.2 + - + +
138B LYS* 4.0 17.8 + - - +
139B LEU* 4.0 19.2 - - + +
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Residues in contact with LEU 14 (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 HIS 3.6 1.0 + - - -
13A GLN* 1.3 71.5 - - - +
15A VAL* 1.3 61.4 + - - +
16A PRO* 4.9 0.2 - - - +
20A LEU* 3.9 18.8 - - + -
29A TYR* 4.3 6.5 - - + -
31A ARG* 3.6 50.7 + - + +
32A GLY 3.4 29.2 - - - +
33A LEU* 4.0 8.1 - - + -
104A ALA 4.3 12.3 - - - +
145A GLY* 3.6 19.7 - - - +
146A GLU* 3.0 13.3 + - - +
147A GLY* 4.1 6.1 - - - +
148A ILE* 4.1 18.6 - - + -
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLN* 4.2 25.4 - - + +
14A LEU* 1.3 78.2 - - - +
16A PRO* 1.4 81.9 - - + +
18A ARG* 3.7 21.1 + - + -
31A ARG* 3.8 5.8 - - - -
32A GLY* 2.8 34.4 + - - +
34A LEU* 3.9 26.0 - - + -
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Residues in contact with PRO 16 (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 LEU 4.9 0.4 - - - +
15A VAL* 1.4 102.6 - - + +
17A GLY* 1.3 62.2 + - - +
18A ARG* 3.4 1.0 + - - +
30A GLU 4.0 14.4 - - - +
31A ARG* 3.9 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