Contacts of the strand formed by residues 17 - 25 (chain B) in PDB entry 1TE6
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 PRO 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLU* 3.6 26.7 - - + +
10B ILE 3.2 8.1 - - - +
11B LEU* 3.8 2.7 - - + -
12B ASP* 4.9 0.9 - - - +
16B ASN* 1.3 89.4 - - + +
18B THR* 1.3 61.9 + - - +
49B ARG* 2.8 28.9 + - - -
56B TYR* 3.4 54.5 - - + -
59B LYS* 3.6 24.7 - - + +
60B GLY* 4.0 1.6 - - - -
61B VAL* 4.2 3.4 - - - +
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Residues in contact with THR 18 (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 GLU* 3.5 6.6 - - - -
10B ILE* 2.8 52.8 + - + +
12B ASP* 4.2 14.6 - - + +
16B ASN 4.5 1.3 - - - -
17B PRO* 1.3 78.0 - - - +
19B VAL* 1.3 67.4 + - - +
34B VAL* 2.6 35.2 + - - +
35B PRO 4.2 5.7 + - - -
36B SER 5.6 0.2 - - - -
49B ARG* 5.1 5.5 + - - +
61B VAL* 3.6 13.4 - - - +
108B ASN* 5.3 3.0 + - - +
375B THR* 3.8 15.0 - - + -
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Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ALA* 4.7 1.8 - - + -
8B ARG 3.9 4.9 - - - +
18B THR* 1.3 82.5 + - - +
20B GLU* 1.3 65.5 + - - +
21B VAL* 4.0 11.4 - - + -
32B ALA 4.2 0.2 - - - +
33B ALA* 3.3 3.3 - - - +
34B VAL* 2.9 37.2 + - + +
61B VAL* 4.1 7.4 - - + -
64B ALA* 3.8 18.6 - - + -
65B VAL* 4.6 5.4 - - + -
68B ILE* 3.7 27.1 - - + -
108B ASN* 3.7 46.2 - - + +
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ARG* 2.7 47.3 + - - -
7B ALA* 3.1 6.4 - - - +
8B ARG* 2.7 67.0 + - + +
10B ILE* 3.6 30.4 - - + +
19B VAL* 1.3 75.8 - - - +
21B VAL* 1.3 66.7 + - - +
22B ASP* 4.4 3.4 - - - +
31B ARG* 3.9 12.9 - - - -
32B ALA 3.3 13.5 - - - +
33B ALA* 4.2 4.6 - - - +
376B GLU* 4.9 0.9 - - - +
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Residues in contact with VAL 21 (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 ILE* 3.8 28.0 - - + -
6B TRP 3.6 4.5 - - - +
7B ALA* 3.9 3.1 - - + -
19B VAL* 4.0 1.8 - - + -
20B GLU* 1.3 78.3 - - - +
22B ASP* 1.3 72.3 + - - +
23B LEU* 5.0 0.9 - - + -
30B PHE 3.6 1.0 - - - +
31B ARG* 3.0 25.1 - - - +
32B ALA 2.9 13.9 + - - -
68B ILE* 3.8 26.7 - - + -
112B GLY* 3.6 34.8 - - - +
113B VAL* 3.8 7.6 - - + +
116B ALA* 4.2 13.6 - - + +
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Residues in contact with ASP 22 (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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4B LYS 3.7 1.0 - - - +
5B ILE* 3.3 5.5 - - - -
6B TRP* 2.8 40.9 + - + +
8B ARG* 3.1 27.7 + - - -
20B GLU* 4.4 0.2 - - - +
21B VAL* 1.3 75.8 - - - +
23B LEU* 1.3 59.2 + - - +
24B TYR* 3.9 18.6 + - + -
29B LEU* 3.5 17.0 - - + +
30B PHE 3.5 3.6 - - - -
31B ARG* 2.8 50.6 + - - +
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Residues in contact with LEU 23 (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 ILE* 3.6 13.9 - - + -
4B LYS 3.6 0.7 - - - -
5B ILE* 3.4 33.4 - - + -
21B VAL* 5.4 0.2 - - + -
22B ASP* 1.3 73.4 - - - +
24B TYR* 1.3 67.1 + - - +
25B THR* 3.6 26.7 - - + -
28B GLY 3.6 0.3 - - - +
29B LEU* 3.7 0.9 - - - -
30B PHE* 2.6 51.2 + - + +
83B VAL* 4.0 4.5 - - + -
113B VAL* 5.0 2.2 - - + -
116B ALA* 3.6 30.7 - - + +
117B VAL* 4.3 18.4 - - + +
120B ALA* 3.8 10.8 - - + -
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Residues in contact with TYR 24 (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 ILE* 3.6 3.1 - - - +
3B GLU* 2.7 41.4 + - + +
4B LYS* 2.8 55.8 + - + +
6B TRP* 5.2 3.4 - - + -
22B ASP* 3.9 21.3 + - + -
23B LEU* 1.3 74.9 - - - +
25B THR* 1.3 64.1 + - - +
28B GLY 3.4 13.0 - - - -
29B LEU* 3.5 38.3 - - + +
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Residues in contact with THR 25 (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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1B SER 3.9 15.0 - - - +
2B ILE* 4.4 0.4 - - - -
3B GLU* 3.8 18.2 - - - +
23B LEU* 3.6 19.1 - - + -
24B TYR* 1.3 81.6 - - - +
26B ALA* 1.3 65.4 + - - +
27B LYS* 3.1 14.9 + - - +
28B GLY* 2.9 17.0 + - - +
30B PHE* 3.1 21.4 - - + -
83B VAL* 4.0 22.2 - - + -
120B ALA* 4.1 7.6 + - + -
124B GLU* 5.4 4.5 - - - -
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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