Contacts of the strand formed by residues 19 - 26 (chain A) in PDB entry 1E3H
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 THR 19 (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* 3.6 26.5 - - + -
12A ILE 3.3 13.9 - - - +
13A ASP* 3.6 20.3 + - + -
18A GLY* 1.3 73.6 - - - -
20A ARG* 1.3 69.3 + - - +
21A THR* 4.9 2.9 - - - +
42A ASP* 4.7 2.3 - - - +
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Residues in contact with ARG 20 (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 ILE* 2.9 44.5 + - + +
14A ASN* 3.3 28.9 - - - +
17A PHE 3.2 27.3 + - - -
18A GLY 4.1 3.0 + - - -
19A THR* 1.3 78.1 - - - +
21A THR* 1.3 67.8 + - - +
41A LEU* 4.2 13.4 - - + +
42A ASP* 3.3 24.7 - - - +
169A VAL* 4.0 1.8 - - - +
170A ALA 3.6 1.2 + - - -
171A PHE* 3.1 29.8 + - + -
172A PRO* 3.7 3.0 - - - +
173A THR* 3.7 11.1 - - - +
176A GLU* 2.5 37.8 + - - -
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Residues in contact with THR 21 (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 GLU* 3.9 34.3 - - + +
10A ALA 3.6 13.0 - - - +
11A VAL* 4.5 12.4 - - + +
12A ILE* 5.0 0.2 - - - -
19A THR* 4.9 2.8 - - - +
20A ARG* 1.3 79.8 + - - +
22A ILE* 1.3 78.0 + - - +
23A ARG* 3.9 3.7 + - + +
40A TYR 3.5 1.0 - - - +
41A LEU* 3.4 3.7 - - - +
42A ASP* 2.8 44.1 + - - -
43A ASP* 4.8 2.4 + - - -
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Residues in contact with ILE 22 (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 GLU* 3.7 1.6 - - - -
10A ALA* 3.0 31.2 + - + +
12A ILE* 4.6 4.3 - - + -
21A THR* 1.3 73.9 - - - +
23A ARG* 1.3 60.4 + - - +
24A PHE* 3.8 31.2 + - + -
39A ALA* 4.5 10.3 - - + -
40A TYR 3.1 12.1 - - - +
41A LEU* 3.8 29.2 - - + -
136A VAL* 4.3 9.0 - - + -
139A ASN* 5.1 4.7 - - + +
171A PHE* 3.7 44.2 - - + -
239A LEU* 4.1 15.0 - - + -
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Residues in contact with ARG 23 (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 TYR* 3.2 54.6 - - + +
8A ALA 3.6 7.6 - - - +
9A GLU* 3.3 38.7 + - - +
21A THR* 3.8 4.2 - - + +
22A ILE* 1.3 73.7 - - - +
24A PHE* 1.3 67.7 + - - +
39A ALA* 3.3 4.4 - - - -
40A TYR* 2.8 56.3 + - + +
43A ASP* 3.1 29.3 + - - +
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Residues in contact with PHE 24 (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 TYR* 3.2 28.3 - - - -
8A ALA* 2.8 21.9 + - + +
10A ALA* 4.5 4.5 - - + -
22A ILE* 3.8 23.1 - - + -
23A ARG* 1.3 75.4 - - - +
25A GLU* 1.3 62.7 + - - +
38A VAL 3.3 11.9 - - - +
39A ALA* 4.3 10.1 - - + -
139A ASN* 3.7 44.6 - - + -
140A ALA* 5.2 0.2 - - - -
143A ALA* 4.1 16.4 - - + -
239A LEU* 4.3 4.9 - - + -
242A ALA* 3.9 28.3 - - + -
243A GLN* 3.8 21.5 - - + -
246A LEU* 3.8 22.0 - - + -
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Residues in contact with GLU 25 (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 THR* 3.9 9.0 - - + -
6A HIS 3.3 5.8 - - - -
7A TYR* 3.5 31.4 + - + -
24A PHE* 1.3 78.1 - - - +
26A THR* 1.3 68.0 + - - +
28A ARG* 3.1 40.0 + - - +
29A LEU* 4.3 2.9 + - - +
37A ALA* 3.2 7.6 - - - +
38A VAL* 2.8 48.6 + - + +
40A TYR* 2.8 35.7 + - + -
246A LEU* 4.4 2.0 - - - -
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Residues in contact with THR 26 (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 GLU 4.0 0.7 - - - +
5A THR* 3.5 2.3 - - - +
6A HIS* 2.8 40.3 + - + -
25A GLU* 1.3 80.9 - - - +
27A GLY* 1.3 63.4 + - - +
28A ARG 3.7 2.7 - - - -
36A SER* 2.7 25.7 + - - -
37A ALA* 4.8 0.4 - - - +
38A VAL* 6.1 0.4 - - - -
147A LEU* 3.3 17.2 - - + +
246A LEU* 3.9 26.0 - - + -
250A ALA* 4.2 14.4 - - + -
252A LYS* 3.9 11.7 + - - -
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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