Contacts of the strand formed by residues 50 - 56 (chain A) in PDB entry 2HVY
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 GLY 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A HIS 3.2 11.4 + - - -
47A ILE 3.2 9.7 + - - -
48A GLN 3.5 0.6 - - - -
49A PHE* 1.3 78.8 - - - +
51A VAL* 1.3 63.7 + - - +
96A LEU* 2.8 34.6 + - - +
99A ALA* 3.5 4.1 - - - +
243A ILE* 3.6 9.6 - - - -
244A GLN 3.2 9.2 - - - -
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Residues in contact with VAL 51 (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 GLY* 1.3 79.0 - - - +
52A ILE* 1.3 64.0 + - - +
53A ASN 3.7 0.2 + - - -
93A PRO* 4.1 6.7 - - + -
94A VAL 3.4 24.0 - - - +
95A ALA* 3.8 17.5 - - + +
99A ALA* 4.6 0.2 - - + -
102A VAL* 3.9 16.8 - - + -
106A LEU* 5.3 1.6 - - + -
211A PHE* 3.6 29.8 - - + -
243A ILE* 3.9 1.7 - - - +
244A GLN* 2.7 44.9 + - - +
245A PRO 4.5 1.6 - - - +
246A MET* 4.0 17.5 - - + -
249A ALA* 4.2 6.3 - - + -
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Residues in contact with ILE 52 (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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51A VAL* 1.3 72.4 - - - +
53A ASN* 1.3 60.1 + - - +
54A LEU* 3.2 23.9 + - + +
69A ILE* 4.0 21.5 - - + -
73A LEU* 4.2 3.1 - - + -
92A LEU 3.5 0.2 - - - +
93A PRO* 3.3 3.6 - - - +
94A VAL* 2.8 45.0 + - + +
96A LEU* 3.8 28.9 - - + -
218A ILE* 3.6 26.2 - - + -
223A LEU* 3.8 23.8 - - + -
242A ALA 3.7 8.3 - - - +
243A ILE* 4.0 18.6 - - + -
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Residues in contact with ASN 53 (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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51A VAL 3.7 3.6 + - - -
52A ILE* 1.3 70.7 - - - +
54A LEU* 1.3 58.4 + - - +
91A VAL* 3.4 30.9 - - - +
92A LEU 4.5 0.8 - - - +
93A PRO* 4.7 1.6 - - - -
211A PHE* 3.7 28.5 - - + +
212A LYS 3.0 22.0 + - - +
216A THR* 3.0 35.7 + - - +
217A LEU* 3.3 12.9 + - - +
218A ILE* 2.9 25.1 + - - +
242A ALA 4.4 4.0 + - - -
244A GLN* 4.6 5.0 - - + +
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Residues in contact with LEU 54 (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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52A ILE* 4.0 19.7 - - + -
53A ASN* 1.3 74.5 - - - +
55A ASP* 1.3 64.9 + - - +
56A LYS* 3.5 13.6 + - - -
65A VAL* 3.4 32.5 - - + -
69A ILE* 4.1 9.4 - - + -
90A GLY 3.2 1.7 - - - +
91A VAL* 3.5 4.0 - - - -
92A LEU* 2.7 51.6 + - + +
94A VAL* 4.4 7.0 - - + -
217A LEU* 3.6 2.9 - - - +
218A ILE* 3.3 14.4 - - + +
219A THR 4.1 2.7 - - - +
220A LEU* 4.0 28.9 - - + +
223A LEU* 4.1 14.4 - - + -
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Residues in contact with ASP 55 (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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54A LEU* 1.3 75.4 - - - +
56A LYS* 1.3 62.5 + - - +
57A PRO* 3.5 6.1 - - - +
90A GLY* 3.3 11.8 + - - -
204A ARG* 2.9 44.3 + - - -
217A LEU* 3.7 21.6 - - + +
218A ILE 2.8 20.0 + - - +
219A THR* 4.2 15.8 - - + +
220A LEU 4.6 1.0 + - - -
30C ALA 4.6 1.0 - - - +
32C PRO* 3.4 25.7 - - + +
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Residues in contact with LYS 56 (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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54A LEU* 3.5 6.9 + - - -
55A ASP* 1.3 72.1 - - - +
57A PRO* 1.3 91.9 + - + +
60A PRO 2.8 25.9 + - - -
62A SER* 3.7 22.2 - - - +
65A VAL* 4.0 11.2 - - + -
84A LEU* 3.7 20.9 - - + -
85A ASP 3.6 10.7 + - - -
86A PRO 3.2 9.7 + - - -
88A VAL 3.0 23.3 + - - -
89A SER* 3.2 10.6 - - - -
90A GLY 2.9 34.5 + - - +
92A LEU* 4.0 24.0 - - + -
32C PRO* 3.5 3.0 - - - +
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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