Contacts of the strand formed by residues 3 - 11 (chain B) in PDB entry 2POD
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B LYS* 1.3 72.0 - - - +
4B THR* 1.3 62.2 + - - +
5B GLU 4.0 9.4 - - - +
6B ILE* 4.3 5.4 - - + -
22B VAL* 3.8 26.5 - - + -
23B HIS 3.5 11.0 - - - +
24B THR* 4.2 2.2 - - + -
53B LEU* 3.4 47.8 - - + +
54B ILE* 3.7 12.2 - - + -
55B GLY* 2.7 28.2 + - - -
56B GLU* 2.9 20.5 + - + +
57B ASP 4.8 0.4 - - - -
58B PRO* 3.9 30.7 - - + -
64B HIS* 5.3 0.4 - - - +
91B LEU* 4.1 4.7 - - + -
399B ASP* 3.6 4.3 - - - +
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Residues in contact with THR 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 LYS* 4.0 4.0 - - + +
3B ILE* 1.3 77.4 - - - +
5B GLU* 1.3 61.7 + - - +
23B HIS* 2.8 29.3 + - - +
24B THR 3.4 6.8 + - - -
25B ASP* 3.7 31.4 - - + +
54B ILE* 4.2 4.4 - - - +
398B SER* 3.3 5.5 - - - -
399B ASP* 3.2 39.2 + - - +
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Residues in contact with GLU 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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3B ILE* 3.8 3.3 - - - +
4B THR* 1.3 84.1 + - - +
6B ILE* 1.3 65.7 + - - +
7B GLU* 4.2 3.1 - - - +
23B HIS* 2.7 62.8 + - + +
54B ILE* 4.3 1.5 - - - +
396B ASN* 3.0 34.9 + - - +
397B THR 3.3 15.7 - - - +
398B SER* 3.8 10.1 + - - -
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Residues in contact with ILE 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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3B ILE* 4.3 9.6 - - + -
5B GLU* 1.3 78.2 - - - +
7B GLU* 1.3 65.3 + - - +
20B VAL* 3.9 23.8 - - + -
21B LEU 3.3 2.5 - - - +
22B VAL* 3.9 18.2 - - + -
45B ILE* 3.9 21.8 - - + -
46B HIS* 3.9 2.9 - - + -
50B ALA* 4.1 18.2 - - + +
53B LEU* 3.9 39.3 - - + -
54B ILE* 4.4 3.3 - - + +
87B LEU* 4.3 5.2 - - + -
396B ASN* 3.6 2.8 - - - -
397B THR* 2.9 44.1 + - + +
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Residues in contact with GLU 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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5B GLU* 4.2 3.1 - - - +
6B ILE* 1.3 74.1 - - - +
8B THR* 1.3 61.5 + - - +
9B LEU* 4.4 8.1 - - + +
19B TRP 4.5 0.2 - - - -
20B VAL* 3.2 6.0 - - - +
21B LEU* 2.7 55.9 + - + +
23B HIS* 2.8 29.5 + - - +
387B ARG* 2.8 31.7 + - - -
394B VAL* 5.0 6.1 - - + +
395B ARG 3.4 6.2 - - - +
396B ASN* 3.4 28.6 + - + +
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Residues in contact with THR 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 GLU* 1.3 77.3 - - - +
9B LEU* 1.3 64.9 + - - +
10B ARG 4.2 0.4 - - - -
18B LEU* 3.8 10.5 - - + -
19B TRP 3.4 3.1 - - - -
20B VAL* 4.2 9.0 - - + -
42B GLU* 2.6 33.4 + - + -
45B ILE* 4.2 29.4 - - + -
46B HIS* 2.7 32.4 + - + +
393B ALA 3.7 0.5 - - - +
394B VAL* 3.4 6.9 - - - -
395B ARG* 3.0 30.7 + - - +
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Residues in contact with LEU 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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7B GLU* 4.4 9.0 - - + +
8B THR* 1.3 82.8 - - - +
10B ARG* 1.3 62.5 + - - +
11B PRO* 3.5 6.0 - - - +
18B LEU* 3.7 4.2 - - - +
19B TRP* 2.9 51.3 + - + +
21B LEU* 4.4 17.3 - - + -
382B LEU* 3.7 27.4 - - + -
386B ILE* 4.4 15.3 - - + -
387B ARG* 3.7 28.7 - - - +
392B ILE* 3.7 16.8 - - + -
393B ALA 3.8 2.7 - - - -
394B VAL* 3.8 8.1 - - + -
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Residues in contact with ARG 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 LEU* 1.3 70.3 - - - +
11B PRO* 1.3 67.3 - - - +
12B GLU* 3.5 3.5 + - - +
15B PRO 5.7 0.9 - - - +
17B LEU 4.5 0.9 - - - +
18B LEU* 3.8 16.4 - - + -
38B ALA* 4.0 21.8 - - + -
39B CYS* 3.6 36.0 - - - +
42B GLU* 2.7 38.5 + - - +
392B ILE* 3.9 2.4 - - - +
393B ALA* 2.9 57.4 + - - +
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Residues in contact with PRO 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 LEU 3.5 10.8 - - - +
10B ARG* 1.3 83.3 - - - +
12B GLU* 1.3 59.6 + - - +
13B GLU* 3.2 6.3 - - + +
14B PHE* 3.0 38.4 - - + +
15B PRO* 3.6 3.1 - - - +
17B LEU* 3.6 25.8 - - + +
19B TRP* 3.6 25.4 - - + -
390B LEU* 3.8 24.5 - - + -
391B THR 3.5 7.9 - - - +
392B ILE* 3.9 9.6 - - + -
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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