Contacts of the helix formed by residues 1003 - 1010 (chain A) in PDB entry 4QUU
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 ASP1003 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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999A ARG 4.0 8.3 - - - +
1000A LEU 3.1 14.6 + - - +
1001A ALA 4.3 2.6 - - - +
1002A ILE* 1.3 78.9 - - - +
1004A LYS* 1.3 67.8 + - - +
1005A ARG* 2.8 55.6 + - - +
1006A PHE* 2.9 32.5 + - + +
1007A ARG* 3.8 3.8 + - - -
1084A THR* 5.7 1.0 - - - +
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Residues in contact with LYS1004 (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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1002A ILE 3.4 5.7 + - - +
1003A ASP* 1.3 74.8 + - - +
1005A ARG* 1.3 84.9 + - - +
1006A PHE 3.2 0.7 + - - -
1007A ARG* 3.5 7.5 + - - +
1204A EDO 2.6 34.6 + - - +
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Residues in contact with ARG1005 (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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1003A ASP* 2.8 38.1 + - - +
1004A LYS* 1.3 98.4 - - - +
1006A PHE* 1.3 86.3 + - + +
1007A ARG 3.4 1.4 + - - -
1008A VAL* 4.8 2.3 + - - +
1009A PHE* 4.7 1.6 - - - -
1076A HIS* 6.3 1.0 - - - -
1077A ARG* 3.3 48.4 + - + +
1080A ALA* 3.9 19.4 - - - +
1084A THR* 4.0 13.7 + - - +
1204A EDO 4.4 2.3 - - - -
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Residues in contact with PHE1006 (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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1000A LEU* 3.3 41.3 - - + +
1003A ASP* 2.9 25.3 + - + +
1005A ARG* 1.3 111.0 - - + +
1007A ARG* 1.3 65.2 + - - +
1008A VAL 3.2 2.5 - - - -
1009A PHE* 2.9 31.3 + + + +
1010A THR* 3.5 8.9 + - - +
1031A LEU* 4.7 2.6 - - + +
1077A ARG 3.4 14.8 - - - -
1080A ALA* 3.7 12.1 - - + -
1081A LEU* 3.4 56.3 - - + -
1084A THR* 4.0 4.5 - - + -
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Residues in contact with ARG1007 (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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1001A ALA 5.5 0.7 - - - -
1003A ASP 3.8 2.9 + - - +
1004A LYS* 3.5 16.0 + - - +
1005A ARG 3.4 2.6 - - - -
1006A PHE* 1.3 75.6 - - - +
1008A VAL* 1.3 61.9 + - - +
1010A THR* 2.7 38.2 + - + +
1011A LYS 4.5 0.3 + - - -
1204A EDO 3.9 25.5 - - - +
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Residues in contact with VAL1008 (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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1005A ARG 4.8 5.4 - - - +
1007A ARG* 1.3 78.6 - - - +
1009A PHE* 1.3 92.8 + - + +
1010A THR 3.4 0.6 + - - -
1011A LYS 4.1 9.9 + - - +
1013A VAL* 5.6 1.2 - - - +
1074A ILE* 4.9 16.6 - - + -
1077A ARG* 5.3 8.1 - - - +
1204A EDO 4.2 10.6 + - - +
1210A EDO 6.1 0.7 - - - +
5B ALY 4.0 33.8 - - + +
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Residues in contact with PHE1009 (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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1006A PHE* 2.9 24.6 + + + +
1008A VAL* 1.3 100.5 - - + +
1010A THR* 1.3 52.5 + - - +
1011A LYS 3.4 3.8 - - - -
1030A ASP* 3.4 8.0 - - - +
1031A LEU* 2.8 39.4 + - + +
1056A ILE* 3.6 28.9 - - + -
1060A ALA* 3.9 20.2 - - + -
1074A ILE* 3.9 9.4 - - + -
1077A ARG* 3.8 13.7 - - + -
1078A ALA* 3.5 41.5 - - + -
1081A LEU* 4.1 16.2 - - + -
5B ALY 4.2 13.2 - - + -
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Residues in contact with THR1010 (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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1001A ALA* 3.6 38.8 - - + +
1006A PHE 3.5 15.5 - - - +
1007A ARG* 2.7 30.7 + - + +
1009A PHE* 1.3 79.8 - - - +
1011A LYS* 1.3 77.8 + - - +
1030A ASP* 3.8 2.2 - - - -
1031A LEU* 4.2 7.2 - - + -
1032A SER* 3.3 25.9 + - - -
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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