Contacts of the strand formed by residues 45 - 54 (chain B) in PDB entry 3GJ0
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 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B TYR* 3.6 6.5 - - - -
40B VAL* 3.0 40.0 + - + -
43B LEU* 3.7 24.9 - - + +
44B GLY* 1.3 77.8 - - - +
46B GLU* 1.3 71.5 + - - +
47B VAL* 4.1 7.9 - - + -
64B TRP* 3.8 36.8 - - + -
65B ASP 3.3 29.8 - - - +
67B ALA* 4.4 1.3 - - - +
79B TYR* 4.2 9.2 - - + -
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 5.3 2.6 - - - +
28B LYS* 5.1 4.3 - - - -
37B LYS* 3.7 35.3 + - + +
38B LYS 3.4 4.9 - - - +
39B TYR* 3.9 26.8 - - + +
45B VAL* 1.3 76.7 - - - +
47B VAL* 1.3 60.5 + - - +
48B HIS* 3.5 22.9 + - + -
63B VAL 3.4 2.4 - - - +
65B ASP* 2.9 38.7 + - + +
66B THR 5.1 0.6 - - - +
67B ALA* 5.9 6.7 - - + -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LYS* 3.2 2.5 - - - -
38B LYS* 2.8 49.5 + - + +
40B VAL* 4.7 7.4 - - + -
45B VAL* 4.1 14.1 - - + -
46B GLU* 1.3 73.0 - - - +
48B HIS* 1.3 61.2 + - - +
49B PRO* 3.5 4.8 - - + +
62B ASN* 3.8 24.7 - - + +
63B VAL 3.3 3.4 - - - +
64B TRP* 3.7 51.8 - - + +
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Residues in contact with HIS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 5.9 0.2 - - + -
27B VAL* 3.7 46.8 - - + +
28B LYS* 4.2 4.6 - - + +
33B GLY 3.4 22.7 - - - +
34B GLU* 3.2 25.0 + - - -
37B LYS* 3.6 16.9 - - + +
46B GLU* 3.5 29.0 + - + -
47B VAL* 1.3 72.9 - - - +
49B PRO* 1.3 64.0 - - - +
50B LEU* 3.2 18.8 + - + +
61B PHE 3.2 5.0 - - - +
62B ASN* 4.4 1.8 - - - -
63B VAL 2.9 33.3 + - - +
65B ASP* 4.3 6.0 - - + +
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Residues in contact with PRO 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B HIS* 4.5 0.7 - - - -
32B THR* 4.7 2.8 - - - +
33B GLY* 3.5 26.0 + - - +
36B GLU* 3.6 41.3 - - + +
38B LYS* 4.9 5.6 - - + +
47B VAL* 3.5 9.6 - - + +
48B HIS* 1.3 81.1 - - - +
50B LEU* 1.3 61.6 + - - +
51B VAL* 3.6 5.9 + - - +
60B LYS* 3.9 19.1 - - + +
62B ASN* 3.5 24.9 - - - +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 4.1 14.1 - - + +
30B HIS* 3.5 36.3 - - + -
33B GLY* 4.0 10.1 - - - -
48B HIS* 3.4 33.4 - - + +
49B PRO* 1.3 71.0 - - - +
51B VAL* 1.3 63.6 + - - +
52B PHE* 3.6 14.5 - - + -
60B LYS* 3.4 1.5 - - - -
61B PHE* 2.8 40.1 + - + +
63B VAL* 3.9 8.5 - - + -
157B PHE* 4.3 6.3 - - + -
161B PHE* 3.7 32.8 - - + -
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B HIS* 3.0 25.8 + - + +
32B THR* 6.4 2.7 - - + -
49B PRO 3.6 5.8 + - - +
50B LEU* 1.3 71.7 - - - +
52B PHE* 1.3 68.8 + - - +
53B HIS* 3.6 36.0 - - + +
58B PRO* 4.6 7.6 - - + -
59B ILE 3.3 11.4 - - - +
60B LYS* 3.6 29.6 - - + -
180B PRO* 4.4 5.0 - - - +
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Residues in contact with PHE 52 (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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30B HIS* 4.3 6.1 - + - -
50B LEU* 3.6 28.0 - - + -
51B VAL* 1.3 78.4 - - - +
53B HIS* 1.3 64.8 + - - +
54B THR 3.8 0.2 + - - -
58B PRO* 3.5 2.1 - - - +
59B ILE* 2.9 41.4 + - + +
61B PHE* 3.8 15.3 - + - -
157B PHE* 4.1 14.8 - + - -
158B GLU* 4.9 2.5 - - - -
161B PHE* 3.5 40.2 - + + -
176B PHE* 3.6 49.1 - + + -
178B ALA 5.6 0.7 - - - -
180B PRO* 3.8 31.9 - - + -
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Residues in contact with HIS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 3.6 26.7 - - + +
52B PHE* 1.3 74.5 - - - +
54B THR* 1.3 62.6 + - - +
57B GLY 4.4 2.0 - - - -
58B PRO* 4.1 19.4 - - + +
176B PHE* 3.4 7.9 - - - +
177B VAL* 2.8 38.2 + - + -
178B ALA* 4.0 17.1 + - + +
180B PRO* 6.5 1.3 - - + -
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Residues in contact with THR 54 (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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52B PHE 4.1 0.4 - - - +
53B HIS* 1.3 77.7 - - - +
55B ASN* 1.3 59.3 + - - +
56B ARG* 2.8 19.7 + - - +
57B GLY* 2.7 41.8 + - - +
59B ILE* 3.7 36.8 - - + +
174B LEU* 4.0 16.3 - - + +
175B GLU 3.1 11.9 - - - -
176B PHE* 3.9 15.7 - - + -
177B VAL* 3.8 9.5 - - - +
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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
------------------------------------------------------------
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