Contacts of the strand formed by residues 34 - 40 (chain A) in PDB entry 2HQQ
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 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE 4.4 0.6 + - - -
18A SER* 3.6 3.3 - - - -
19A LEU* 3.0 49.4 + - - +
32A CYS* 3.4 7.6 - - - +
33A LEU* 1.3 81.5 - - - +
35A GLN* 1.3 63.6 + - - +
36A ARG* 5.7 6.4 + - - +
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Residues in contact with GLN 35 (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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16A VAL* 3.7 25.9 - - + +
17A ILE 3.1 13.0 - - - +
18A SER* 3.9 17.2 + - - +
32A CYS* 6.0 1.3 - - + -
34A SER* 1.3 77.1 - - - +
36A ARG* 1.3 65.1 + - - +
37A TRP* 5.7 3.8 + - + -
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Residues in contact with ARG 36 (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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16A VAL* 3.7 1.9 - - - +
17A ILE* 2.8 72.0 + - + +
19A LEU* 5.5 6.7 - - - +
34A SER* 5.3 7.0 + - - +
35A GLN* 1.3 76.1 - - - +
37A TRP* 1.3 70.7 + - - +
38A GLN* 2.6 32.9 + - - +
101A ILE* 4.5 2.8 - - - +
252A ASP* 3.7 21.6 + - - -
292A GLN* 3.2 34.1 + - - +
293A GLY* 4.1 1.8 - - - +
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Residues in contact with TRP 37 (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 LEU* 3.8 31.6 - - + -
15A ASP 3.4 3.6 - - - -
16A VAL* 4.0 26.8 - - + +
35A GLN* 5.7 3.8 + - + -
36A ARG* 1.3 83.5 - - - +
38A GLN* 1.3 60.6 + - - +
67A HIS* 5.0 4.5 - - + -
68A VAL* 4.2 19.5 - - + -
71A PHE* 3.7 55.4 - + + -
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Residues in contact with GLN 38 (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 LEU* 4.0 0.8 - - - -
15A ASP* 2.9 35.4 + - + +
17A ILE* 3.5 15.5 - - + -
36A ARG* 2.6 34.7 + - - +
37A TRP* 1.3 74.6 - - - +
39A ARG* 1.3 75.5 + - - +
45A ASN* 5.3 1.0 + - - +
71A PHE* 4.2 5.4 - - - -
252A ASP* 5.0 0.4 + - - -
254A LEU* 3.5 29.3 + - - +
293A GLY* 3.9 13.2 - - - -
294A PHE* 3.8 27.4 - - + -
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Residues in contact with ARG 39 (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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12A VAL* 3.9 13.0 - - + -
13A VAL 3.8 4.0 - - - -
14A LEU* 5.1 0.2 - - - +
15A ASP* 4.3 0.2 - - - +
38A GLN* 1.3 85.8 + - - +
40A GLY* 1.3 62.9 + - - +
44A SER* 3.0 39.3 + - - +
45A ASN* 3.3 11.0 + - - +
48A THR* 2.7 32.3 + - - +
71A PHE* 3.9 7.8 - - + -
72A VAL* 3.6 31.2 - - + -
75A ASP* 2.8 43.3 + - + +
76A LEU* 3.3 36.3 - - - +
79A TYR* 3.5 21.8 - - - +
294A PHE* 4.8 2.1 - - - -
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Residues in contact with GLY 40 (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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12A VAL* 3.6 0.9 - - - +
13A VAL 2.7 28.5 + - - +
15A ASP* 3.4 18.2 - - - -
38A GLN 3.4 1.6 + - - -
39A ARG* 1.3 74.7 - - - +
41A GLY* 1.3 61.2 + - - -
44A SER* 2.8 22.9 + - - -
45A ASN* 3.3 12.1 - - - -
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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