Contacts of the strand formed by residues 13 - 18 (chain T) in PDB entry 3L9J
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 VAL 13 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9T SER* 6.2 0.2 - - - +
11T LYS* 3.7 12.1 - - + +
12T PRO* 1.3 74.8 - - - +
14T ALA* 1.3 67.3 + - - +
15T HIS* 6.0 0.2 - - + -
36T LEU* 4.3 26.7 - - + -
37T LEU* 3.7 0.7 + - - -
38T ALA* 2.9 51.3 + - + +
39T ASN* 4.4 2.9 - - - +
41T VAL* 3.7 5.5 - - - +
154T ILE 3.3 12.3 - - - +
155T ILE* 4.6 18.2 - - + -
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Residues in contact with ALA 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13T VAL* 1.3 78.5 - - - +
15T HIS* 1.3 62.6 + - - +
16T VAL* 4.7 1.3 - - + -
36T LEU* 3.2 15.5 - - - +
37T LEU* 4.0 4.0 - - + -
41T VAL* 4.0 14.1 - - + -
48T LEU* 3.9 34.5 - - + -
59T TYR* 3.9 2.8 + - - -
153T GLY* 3.0 4.0 - - - -
154T ILE* 2.9 33.2 + - + +
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Residues in contact with HIS 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13T VAL* 6.0 0.4 - - + -
14T ALA* 1.3 76.1 - - - +
16T VAL* 1.3 61.0 + - - +
17T VAL* 4.2 12.5 - - + +
34T ASN 3.7 20.8 + - - +
35T ALA* 3.2 10.4 - - - +
36T LEU* 2.9 50.5 + - + +
59T TYR* 2.6 26.6 + + - +
151T TYR* 3.5 46.1 - + + +
152T PHE 3.5 4.2 + - - -
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Residues in contact with VAL 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15T HIS* 1.3 80.4 - - - +
17T VAL* 1.3 62.5 + - - +
28T TRP* 3.7 23.8 - - + -
29T LEU 3.4 20.6 - - - +
30T ASN* 3.9 14.4 - - + -
36T LEU 3.9 11.9 - - - +
37T LEU* 4.6 2.5 - - + -
43T LEU* 4.4 6.5 - - + -
48T LEU* 4.3 24.0 - - + -
151T TYR* 3.1 6.2 - - - +
152T PHE* 2.7 58.9 + - + +
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Residues in contact with VAL 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15T HIS* 4.2 23.3 - - + +
16T VAL* 1.3 79.6 - - - +
18T ALA* 1.3 72.9 + - - +
19T ASN 3.4 0.2 + - - -
20T PRO* 5.6 0.9 - - + -
28T TRP* 3.5 5.8 - - - -
29T LEU* 2.8 39.6 + - + +
32T ARG* 4.2 27.8 - - + -
33T ALA 5.6 2.0 - - - +
34T ASN 4.9 3.4 - - - +
35T ALA* 4.6 8.3 - - + -
148T GLY* 6.0 5.4 - - - +
150T VAL 3.5 13.9 - - - +
151T TYR* 4.4 0.9 - - + -
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Residues in contact with ALA 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17T VAL* 1.3 79.6 - - - +
19T ASN* 1.3 64.6 + - - +
20T PRO* 3.1 11.6 - - - +
25T GLN 5.7 0.2 - - - +
26T LEU* 3.8 14.8 - - + -
27T GLN 3.6 7.2 - - - +
28T TRP* 3.8 2.2 - - - -
144T PHE* 3.6 34.3 - - + +
150T VAL* 3.3 31.6 + - + -
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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
------------------------------------------------------------
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