Contacts of the strand formed by residues 12 - 20 (chain A) in PDB entry 5HKE
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 ASN 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU 3.6 3.1 - - - -
8A ASN* 2.7 32.9 + - - +
9A GLY 4.5 1.6 + - - +
11A SER* 1.3 84.3 + - - +
13A TYR* 1.3 58.3 + - - +
146A ARG* 3.4 47.3 + - + +
279A ASP* 3.7 4.3 - - - +
280A LEU* 2.8 36.2 + - + +
281A ASP* 3.2 29.2 + - - +
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Residues in contact with TYR 13 (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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6A THR* 3.2 8.0 - - - +
7A LEU* 2.8 52.9 + - + +
8A ASN* 5.5 0.7 + - - -
9A GLY 4.2 3.4 - - - -
11A SER* 3.2 44.1 + - - -
12A ASN* 1.3 76.2 - - - +
14A PHE* 1.3 63.7 + - - +
241A VAL* 3.6 11.0 - - + +
244A ASP* 2.7 45.5 + - + +
245A ILE* 4.1 16.8 - - + -
248A PHE* 3.6 20.9 - + + -
277A CYS* 3.8 18.8 - - - -
278A TYR 3.1 11.9 - - - +
279A ASP* 3.9 14.8 - - + -
280A LEU* 4.4 5.0 - - - +
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Residues in contact with PHE 14 (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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4A ALA* 5.2 0.2 - - + -
5A ILE 3.4 12.3 - - - -
6A THR* 4.3 3.1 - - + -
13A TYR* 1.3 79.0 - - - +
15A GLY* 1.3 61.8 + - - +
16A ARG* 6.4 0.2 - - + -
66A ASP* 4.9 1.1 - - + -
67A ALA 3.9 8.3 - - - -
68A ILE* 4.1 4.7 - - + -
74A GLY* 3.8 11.7 - - - -
75A MET 3.5 40.2 - - - -
76A ALA* 3.7 13.5 - - + -
142A LEU* 4.0 29.2 - - + -
144A ALA* 3.7 24.7 - - + -
248A PHE* 3.7 4.0 - - - -
278A TYR* 2.7 60.1 + + - +
280A LEU* 4.0 19.1 - - + -
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Residues in contact with GLY 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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4A ALA* 3.3 3.4 - - - +
5A ILE* 2.9 32.2 + - - +
14A PHE* 1.3 82.6 - - - +
16A ARG* 1.3 65.0 + - - +
248A PHE* 3.5 8.8 - - - -
252A LEU* 4.7 0.7 - - - -
276A ASN* 3.2 23.6 - - - -
278A TYR* 4.4 4.0 - - - -
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Residues in contact with ARG 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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2A OCS 3.2 27.3 + - - -
3A THR 3.1 14.4 - - - +
4A ALA* 3.8 12.3 - - + -
14A PHE* 6.3 0.4 - - + -
15A GLY* 1.3 76.3 - - - +
17A ASN* 1.3 79.3 + - - +
18A LEU* 3.5 16.2 - - - +
65A PHE* 3.0 26.1 + - - +
66A ASP* 2.8 46.4 + - + +
76A ALA* 4.1 6.4 - - + +
77A GLY 2.9 21.2 + - - -
78A LEU* 3.7 10.6 - - - +
252A LEU* 3.9 10.1 - - - +
274A TYR* 3.8 9.8 - - - +
275A SER* 3.2 3.1 - - - -
276A ASN* 2.8 40.7 + - - +
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Residues in contact with ASN 17 (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 OCS 3.4 4.3 + - - -
3A THR* 2.8 31.2 + - - +
16A ARG* 1.3 83.2 + - - +
18A LEU* 1.3 59.0 + - - +
19A ASP* 3.6 14.6 - - - +
252A LEU* 3.0 37.9 + - - +
255A VAL* 3.9 17.8 + - - +
256A GLU* 4.0 12.7 - - - +
272A THR* 3.7 9.4 - - + -
274A TYR 3.4 3.6 - - - -
275A SER* 2.7 29.5 + - - -
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Residues in contact with LEU 18 (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 OCS 3.2 18.2 - - - +
16A ARG* 3.5 22.7 - - - +
17A ASN* 1.3 70.2 - - - +
19A ASP* 1.3 56.5 + - - +
20A LEU* 3.8 34.8 - - + -
26A GLU* 4.2 7.0 - - - +
65A PHE* 3.8 24.5 - - + -
77A GLY 5.5 0.2 - - - +
272A THR* 3.5 2.1 - - - -
273A VAL* 2.8 37.7 + - + +
274A TYR* 2.9 48.7 + - + -
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Residues in contact with ASP 19 (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 OCS 2.8 48.4 + - - +
3A THR* 4.4 1.0 + - - -
17A ASN* 3.6 9.7 - - - +
18A LEU* 1.3 72.7 - - - +
20A LEU* 1.3 69.9 + - - +
79A ASN* 4.2 1.4 - - - +
224A ARG* 3.9 7.8 + - - -
255A VAL 4.6 2.3 - - - +
257A GLN* 3.0 35.9 + - - +
270A GLU* 3.7 11.3 - - + +
271A TYR 3.2 6.5 - - - +
272A THR* 2.6 32.7 + - - -
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Residues in contact with LEU 20 (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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18A LEU* 3.8 35.3 + - + -
19A ASP* 1.3 82.5 - - - +
21A ASP* 1.3 59.2 + - - +
22A PHE* 3.3 36.7 + - + +
24A TYR* 3.6 32.3 - - + +
26A GLU* 4.6 1.6 - - - +
79A ASN* 3.7 19.5 - - - +
270A GLU* 3.9 6.9 - - - +
271A TYR* 2.9 37.6 + - - +
273A VAL* 4.1 3.8 - - + +
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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