Contacts of the strand formed by residues 12 - 16 (chain A) in PDB entry 1HNY
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 12 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG 3.7 0.6 - - - -
11A THR* 1.3 78.3 + - - +
13A ILE* 1.3 71.2 + - - +
37A PHE* 4.5 3.8 - - - +
38A GLY* 2.9 33.0 + - - +
39A GLY 3.3 0.5 + - - +
329A LEU* 3.7 14.0 - - - +
335A PHE* 4.1 2.8 - - - -
336A THR* 2.8 28.9 + - - -
338A VAL* 4.9 3.6 - - - -
395A VAL* 4.5 25.9 + - - +
398A ARG* 4.0 4.2 - - - -
399A ASN* 4.6 1.0 + - - -
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 4.6 0.7 - - + -
12A SER* 1.3 82.4 - - - +
14A VAL* 1.3 54.7 - - - +
37A PHE* 5.3 1.3 - - - -
38A GLY 4.5 0.9 - - - -
39A GLY 3.2 16.2 - - - +
41A GLN* 4.1 15.9 - - + +
94A TYR* 3.4 37.2 - - + +
229A PHE* 5.6 0.9 - - + -
231A TYR* 3.3 34.8 - - + +
293A LEU* 5.0 3.8 - - + -
335A PHE* 3.7 24.5 - - + -
336A THR 3.0 6.3 + - - +
337A ARG* 3.1 24.8 - - + -
338A VAL* 2.8 33.9 + - - +
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 1.3 75.0 - - - +
15A HIS* 1.3 65.3 + - - +
16A LEU* 3.5 8.7 + - + -
32A LEU* 3.8 19.1 - - + -
37A PHE* 3.6 25.6 - - + -
39A GLY 2.8 19.1 + - - +
40A VAL* 3.2 12.3 - - + +
41A GLN* 2.8 25.8 + - - -
337A ARG* 4.7 0.7 - - - -
338A VAL* 3.3 18.6 - - + +
340A SER* 4.0 15.5 - - - -
386A HIS* 3.7 27.1 - - + -
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Residues in contact with HIS 15 (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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13A ILE 4.3 0.2 - - - -
14A VAL* 1.3 70.7 - - - +
16A LEU* 1.3 58.1 + - - +
17A PHE* 3.2 38.5 + + + -
41A GLN* 3.3 46.3 + - + -
42A VAL 4.7 4.7 - - - -
43A SER* 4.3 9.4 - - - -
62A TYR* 5.2 1.8 + - - -
96A ASP* 5.4 2.2 - - - -
298A ASN* 5.6 0.9 - - + -
299A HIS* 3.8 20.1 + - + -
337A ARG* 4.1 19.4 - - - +
338A VAL 2.8 16.7 + - - +
339A MET* 3.7 28.9 - - + -
340A SER* 3.1 25.1 + - - +
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Residues in contact with LEU 16 (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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14A VAL* 3.5 13.6 + - + -
15A HIS* 1.3 70.0 - - - +
17A PHE* 1.3 65.5 + - - +
18A GLU 3.2 3.1 + - - -
19A TRP* 3.2 46.3 + - + +
24A ILE* 4.1 23.5 - - + +
27A GLU* 4.4 4.0 - - + -
32A LEU* 4.2 12.1 - - + -
40A VAL* 3.8 34.8 - - + -
41A GLN 3.3 12.8 + - - +
43A SER* 4.5 5.0 + - - -
340A SER* 3.7 15.5 - - - +
386A HIS* 3.7 33.0 - - + +
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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