Contacts of the strand formed by residues 56 - 62 (chain D) in PDB entry 2H5X
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 SER 56 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A VAL* 3.0 13.6 - - - +
51D ILE 4.4 1.3 + - - -
53D ARG* 2.7 57.6 + - - +
55D ASP* 1.3 81.8 - - - +
57D MET* 1.3 61.9 + - - +
58D THR* 4.2 11.3 + - - -
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Residues in contact with MET 57 (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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1A MET* 3.3 63.2 + - + +
50A MET* 4.0 19.5 - - + +
52A VAL* 4.3 7.8 - - + +
57A MET* 4.0 29.2 - - - +
57C MET* 4.2 18.4 - - - +
1D MET* 6.4 0.2 - - + -
50D MET* 4.2 16.8 - - + -
51D ILE 3.5 5.4 - - - -
52D VAL* 4.1 21.1 - - + -
53D ARG 5.3 0.2 - - - +
56D SER* 1.3 78.6 - - - +
58D THR* 1.3 60.8 + - - +
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Residues in contact with THR 58 (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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1A MET* 5.2 1.3 - - - +
27D ARG* 5.7 1.1 - - - +
29D ASN* 2.9 33.9 - - - +
49D ALA 3.7 1.0 - - - +
50D MET* 3.6 3.4 - - - +
51D ILE* 3.0 36.2 + - - -
56D SER* 4.4 9.8 - - - -
57D MET* 1.3 80.5 + - - +
59D LEU* 1.3 64.8 + - - +
60D TYR* 3.5 30.8 + - + +
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Residues in contact with LEU 59 (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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1A MET* 3.8 27.2 - - + +
2D ILE* 4.2 17.3 - - + -
5D VAL* 4.1 18.4 - - + -
26D TYR* 4.1 26.0 - - + -
27D ARG 3.7 14.4 + - - +
28D VAL* 3.9 12.0 - - + -
29D ASN* 3.0 32.9 + - - -
48D THR* 4.2 9.6 - - + +
49D ALA 3.9 0.7 - - - -
50D MET* 3.5 39.9 - - + +
57D MET 4.4 0.2 + - - -
58D THR* 1.3 75.6 - - - +
60D TYR* 1.3 60.0 + - - +
61D GLY 4.2 0.2 - - - -
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Residues in contact with TYR 60 (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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28D VAL* 3.9 1.8 - - - -
29D ASN* 3.4 27.4 - - + +
48D THR* 3.0 3.8 - - - -
49D ALA 2.8 44.1 + - - +
51D ILE* 3.6 26.5 - - + -
58D THR* 3.5 30.0 + - + +
59D LEU* 1.3 73.4 - - - +
61D GLY* 1.3 59.3 + - - +
62D PHE* 3.3 13.5 - - + -
71D PHE* 3.6 22.7 - + + -
82D PRO* 3.1 28.5 - - + +
83D ARG* 4.7 4.3 + - - +
86D MET* 3.6 29.8 - - + -
504D GOL 4.8 3.3 + - - -
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Residues in contact with GLY 61 (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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28D VAL* 3.1 21.3 - - - +
29D ASN 2.7 13.2 + - - +
30D ALA* 3.6 20.3 - - - +
34D THR* 4.3 1.4 + - - +
46D LEU* 4.1 9.2 - - - -
47D ILE 3.1 7.0 - - - -
48D THR* 3.7 4.3 - - - -
60D TYR* 1.3 72.6 - - - +
62D PHE* 1.3 74.9 + - - -
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Residues in contact with PHE 62 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D THR* 5.1 5.6 - - + -
34D THR* 4.3 5.2 - - - -
46D LEU* 3.5 10.6 - - - +
47D ILE* 2.6 42.7 + - - +
49D ALA* 4.5 0.2 - - + -
60D TYR* 3.3 28.0 - - + -
61D GLY* 1.3 78.8 - - - -
63D PRO* 1.3 74.8 - - + +
64D ASP 3.4 2.6 + - - +
67D THR* 3.7 29.2 - - + -
68D ARG* 3.5 24.5 - - + +
71D PHE* 3.4 41.7 - + + -
86D MET* 4.0 14.8 - - + -
89D LEU* 3.6 23.6 - - + -
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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