Contacts of the strand formed by residues 3 - 14 (chain A) in PDB entry 1IV4
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 ILE 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ARG* 1.3 74.1 - - - +
4A GLY* 1.3 71.2 + - - +
51A ALA* 3.4 10.9 - - - -
147A VAL* 3.6 12.1 - - + -
148A VAL 3.3 13.2 - - - +
149A LEU* 5.1 5.2 - - + -
203B ILE* 3.4 16.2 - - + -
403C ILE* 3.3 34.5 - - + -
493C GLN* 2.9 36.9 - - + +
495C SER* 4.1 8.2 - - - -
547C VAL* 3.4 22.0 - - + +
549C LEU* 4.0 28.7 - - + +
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Residues in contact with GLY 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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3A ILE* 1.3 78.6 - - - +
5A TYR* 1.3 60.7 + - - -
47A ALA* 3.5 24.1 - - - +
51A ALA* 4.0 4.0 - - - -
147A VAL* 3.3 7.4 - - - +
148A VAL* 2.9 34.5 + - - +
495C SER* 3.4 9.2 - - - -
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Residues in contact with TYR 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 GLY* 1.3 74.5 - - - +
6A GLY* 1.3 58.5 + - - +
7A GLU* 3.7 20.4 + - + -
46A ASP 4.6 0.2 - - - +
47A ALA* 3.9 5.0 + - - +
50A SER* 4.0 10.4 + - - -
145A ARG* 3.4 16.8 - - - -
146A ALA 3.3 23.1 - - - -
147A VAL* 3.6 18.8 - - + -
205B TYR* 3.3 22.5 + + - -
405C TYR* 3.3 25.7 + + - -
495C SER* 2.8 27.1 + - - +
496C LEU 4.9 0.7 - - - +
497C VAL* 3.6 23.4 - - + +
530C THR* 4.4 2.1 + - - -
545C ARG* 3.6 34.2 - - + -
547C VAL* 4.1 22.7 - - + -
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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 TYR* 1.3 77.1 - - - +
7A GLU* 1.3 65.5 + - - +
43A ALA* 3.7 21.6 - - - +
46A ASP* 4.2 6.1 - - - -
47A ALA* 3.6 7.8 - - - +
145A ARG* 3.4 2.3 - - - +
146A ALA 2.8 34.8 + - - +
497C VAL* 3.9 5.4 - - - -
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Residues in contact with GLU 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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5A TYR* 3.7 11.9 - - + +
6A GLY* 1.3 80.5 - - - +
8A ASP* 1.3 63.9 + - - +
43A ALA* 3.8 7.4 - - - +
46A ASP* 3.9 6.8 + - - +
144A ALA 3.3 8.5 - - - +
145A ARG* 3.0 28.9 + - + -
497C VAL* 3.8 28.0 - - + +
499C THR* 4.3 6.6 + - - +
530C THR* 5.3 0.2 + - - -
532C LYS* 3.0 26.6 - - + +
545C ARG* 3.0 52.2 + - - +
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Residues in contact with ASP 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 GLU* 1.3 76.2 - - - +
9A SER* 1.3 73.7 + - - +
10A HIS* 3.0 11.4 + - - -
39A ALA* 3.4 23.7 - - - +
42A HIS* 2.8 22.3 + - + +
43A ALA* 3.9 1.3 - - - +
143A GLN* 3.5 1.7 - - - +
144A ALA 2.9 31.7 + - - +
1561A MG 2.0 27.1 - - - -
1571A MG 2.1 29.6 - - - -
532C LYS* 2.9 6.0 + - - +
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Residues in contact with SER 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 ASP* 1.3 86.8 + - - +
10A HIS* 1.3 75.3 + - - +
39A ALA* 4.8 0.9 - - - -
141A HIS* 4.9 6.2 + - - -
142A VAL 3.1 12.6 - - - -
143A GLN* 4.1 15.9 - - - -
1571A MG 4.0 1.8 - - - -
532C LYS* 4.6 1.8 - - - +
533C THR 4.4 5.5 + - - -
534C SER* 4.0 14.4 + - - -
535C GLU* 3.4 24.7 - - - +
537C LEU* 5.4 3.3 - - - +
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Residues in contact with HIS 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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8A ASP* 3.0 11.2 + - - -
9A SER* 1.3 82.9 + - - +
11A ARG* 1.3 71.3 + - - +
31A ALA* 4.0 8.5 - - + -
32A LEU 4.4 3.0 + - - +
33A ALA* 3.7 16.8 - - + +
35A SER* 3.7 11.2 - - - -
37A GLY* 3.3 34.2 - - - -
39A ALA* 4.3 4.9 - - + -
42A HIS* 3.4 4.4 + - - -
141A HIS* 3.2 7.6 - - - -
142A VAL* 2.9 43.6 + - + +
1561A MG 2.1 32.3 - - - -
1571A MG 4.6 3.6 - - - -
535C GLU* 4.3 13.2 + - - -
1601C C5P 5.5 0.7 - - - -
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Residues in contact with ARG 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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10A HIS* 1.3 74.4 - - - +
12A LEU* 1.3 70.1 + - - +
13A GLU* 4.9 7.0 - - + -
31A ALA* 3.5 4.5 - - - -
32A LEU* 2.9 58.6 + - + +
140A SER* 3.5 20.6 - - - +
141A HIS* 3.6 30.2 + - + -
535C GLU* 3.6 26.6 + - + +
536C GLY* 3.9 18.6 + - - -
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Residues in contact with LEU 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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11A ARG* 1.3 79.3 - - - +
13A GLU* 1.3 71.1 - - - +
18A LEU* 4.4 9.9 - - + -
29A VAL* 4.2 24.9 - - + -
30A GLY* 3.4 27.1 - - - +
31A ALA 4.1 1.6 - - - +
100A LEU* 4.8 5.8 - - + -
101A ASP 5.7 1.6 - - - +
102A ARG* 4.6 10.3 - - + +
139A PRO 4.8 4.7 - - - +
140A SER* 2.6 29.6 + - - +
141A HIS 3.4 36.1 - - - +
142A VAL* 3.7 23.6 - - + +
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Residues in contact with GLU 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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11A ARG* 4.1 8.1 + - + -
12A LEU* 1.3 84.1 - - - +
14A GLU* 1.3 67.9 - - - +
15A GLY 3.4 0.3 + - - -
16A ARG* 2.8 32.6 + - - +
29A VAL* 4.0 5.4 - - - -
30A GLY 2.7 33.8 + - - +
32A LEU* 2.8 43.1 - - + +
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Residues in contact with GLU 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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13A GLU* 1.3 76.7 - - - +
15A GLY* 1.3 60.4 + - - +
16A ARG* 3.5 5.2 + - - +
28A PRO* 3.3 15.9 - - + +
29A VAL* 3.9 5.2 - - + +
102A ARG* 2.6 31.0 + - - +
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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