Contacts of the strand formed by residues 44 - 49 (chain D) in PDB entry 2GJ6
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 GLU 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D TYR* 3.2 3.9 - - - -
36D ARG* 2.6 81.7 + - + +
38D TYR* 4.8 4.7 - - - -
41D LYS* 4.6 6.3 + - - +
42D SER* 4.3 5.2 - - - +
43D PRO* 1.3 74.5 - - - +
45D LEU* 1.3 71.7 + - - +
46D ILE* 3.5 3.0 + - + +
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PHE* 3.9 12.6 - - + -
34D TRP 3.5 16.8 - - - +
35D TYR* 3.7 35.8 - - + +
44D GLU* 1.3 80.3 - - - +
46D ILE* 1.3 64.6 + - - +
47D MET 3.7 17.3 - - - +
48D SER* 4.2 7.4 - - - +
105E GLU* 3.7 45.8 - - + +
106E GLN 4.5 6.7 - - - +
107E TYR* 4.2 13.6 - - + -
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Residues in contact with ILE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TRP* 3.0 21.9 + - + +
36D ARG* 4.1 41.1 - - + +
44D GLU* 4.1 4.9 - - + +
45D LEU* 1.3 80.0 - - - +
47D MET* 1.3 72.8 + - + +
57D ASP* 4.5 7.1 - - - +
62D PHE* 4.0 30.6 - - + -
75D LEU* 4.1 15.5 - - + -
88D TYR* 3.8 34.8 - - + -
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Residues in contact with MET 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PHE* 3.4 4.2 - - - -
34D TRP* 2.9 47.4 + - + +
45D LEU* 3.7 5.1 - - - +
46D ILE* 1.3 87.4 - - + +
48D SER* 1.3 63.7 + - - +
49D ILE 4.3 0.2 - - - -
55D LYS* 3.4 49.4 - - + +
57D ASP* 3.9 26.2 - - + +
62D PHE* 4.0 27.8 - - + +
64D ALA* 3.8 17.3 - - + +
75D LEU* 4.0 13.2 - - + -
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Residues in contact with SER 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D PHE 3.4 5.6 - - - -
33D PHE* 3.3 21.8 - - - -
45D LEU* 4.2 5.9 - - - +
47D MET* 1.3 77.3 - - - +
49D ILE* 1.3 59.7 + - - +
50D TYR* 3.5 28.0 + - - -
55D LYS* 2.6 40.8 + - - +
105E GLU* 3.9 14.1 + - - -
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D PHE* 2.8 55.2 + - + +
34D TRP* 5.5 2.5 - - + -
47D MET 4.3 0.2 - - - -
48D SER* 1.3 75.5 - - - +
50D TYR* 1.3 69.0 + - - +
51D SER 3.6 13.0 - - - +
53D GLY 3.5 25.8 - - - +
54D ASP 4.5 0.2 - - - -
55D LYS* 4.1 17.5 - - + +
64D ALA* 3.9 28.5 - - + +
65D GLN 3.9 4.3 - - - +
66D LEU* 3.7 21.1 - - + +
73D VAL* 4.2 15.7 - - + -
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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