Contacts of the strand formed by residues 56 - 62 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ILE 4.6 1.8 + - - -
52A VAL* 3.7 1.9 - - - +
53A ARG* 3.0 46.2 + - - +
55A ASP* 1.3 81.2 - - - +
57A MET* 1.3 64.7 + - - +
58A THR* 4.2 10.4 + - - -
52B VAL* 2.9 14.0 - - - +
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Residues in contact with MET 57 (chain A).
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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50A MET* 4.6 5.4 - - + -
51A ILE 3.7 3.8 - - - -
52A VAL* 4.1 26.0 - - + -
53A ARG 5.6 1.6 - - - +
56A SER* 1.3 78.3 - - - +
58A THR* 1.3 62.8 + - - +
1B MET* 3.3 53.5 + - - +
50B MET* 4.0 21.3 - - + +
52B VAL* 4.1 10.1 - - + +
57B MET* 3.5 31.2 - - + +
57C MET* 5.0 1.3 - - + -
57D MET* 4.0 25.6 - - + +
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Residues in contact with THR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG* 5.5 5.2 - - - +
29A ASN* 3.0 31.4 - - - +
49A ALA 3.5 1.9 - - - +
50A MET* 3.4 4.8 - - - -
51A ILE* 2.8 42.6 + - - -
56A SER* 4.5 9.0 + - - -
57A MET* 1.3 80.2 + - - +
59A LEU* 1.3 70.0 + - - +
60A TYR* 3.7 23.6 + - + +
1B MET* 5.1 1.1 - - - +
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ILE* 3.9 10.3 - - + -
5A VAL* 4.2 14.8 - - + -
26A TYR* 4.0 28.0 - - + -
27A ARG 3.7 13.7 + - - +
28A VAL* 3.6 9.7 - - + -
29A ASN* 3.0 32.3 + - - +
48A THR* 3.8 22.2 - - + +
49A ALA 3.7 0.2 - - - -
50A MET* 3.6 34.5 - - + +
58A THR* 1.3 75.1 - - - +
60A TYR* 1.3 61.3 + - - +
1B MET* 3.8 30.6 - - + +
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 3.9 1.1 - - - -
29A ASN* 3.5 32.2 + - + +
48A THR* 3.1 2.7 - - - -
49A ALA 2.8 40.4 + - - +
51A ILE* 3.7 27.6 - - + -
58A THR* 3.7 28.3 + - + +
59A LEU* 1.3 74.4 - - - +
61A GLY* 1.3 59.5 + - - +
62A PHE* 3.2 23.4 - - + -
71A PHE* 3.6 10.8 - + + -
82A PRO* 3.3 26.7 - - + +
83A ARG* 4.6 6.8 + - + +
86A MET* 3.5 32.3 - - + -
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Residues in contact with GLY 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 3.1 19.0 - - - +
29A ASN 2.9 16.3 + - - +
30A ALA* 3.8 12.0 - - - +
31A THR 5.2 0.2 + - - -
34A THR* 4.4 1.7 + - - +
46A LEU* 4.0 11.2 - - - -
47A ILE 3.5 5.6 - - - -
48A THR* 4.0 6.7 - - - -
60A TYR* 1.3 72.9 - - - +
62A PHE* 1.3 75.4 - - - -
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Residues in contact with PHE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 6.3 0.2 - - - -
31A THR* 5.8 4.0 - - + -
34A THR* 4.3 6.3 - - - -
46A LEU* 3.8 11.0 - - - +
47A ILE* 2.9 40.4 + - - +
49A ALA* 4.5 0.2 - - + -
60A TYR* 3.2 32.5 - - + -
61A GLY* 1.3 79.1 - - - -
63A PRO* 1.3 76.4 - - + +
64A ASP 3.4 6.4 + - - +
67A THR* 3.7 28.5 - - + -
68A ARG* 3.4 25.4 - - + -
71A PHE* 3.4 33.0 - + + -
86A MET* 4.1 12.8 - - + -
89A LEU* 3.9 22.7 - - + -
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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