Contacts of the helix formed by residues 1034 - 1039 (chain A) in PDB entry 3K72
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 PHE1034 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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918A TYR* 3.3 28.3 - + - -
923A GLU* 3.4 30.2 - - - +
925A GLU 5.3 0.4 - - - -
926A GLU* 4.4 10.7 - - - +
927A LYS* 3.5 38.2 + - + +
928A GLU 4.1 9.6 - - - -
929A SER 4.7 0.7 - - - -
930A HIS* 4.0 23.1 - - + -
1032A LEU 3.5 16.6 - - - -
1033A SER* 1.3 74.4 + - - +
1035A GLY* 1.3 65.4 + - - +
1036A TRP 3.5 1.8 - - - -
1037A VAL* 3.1 28.3 - - + +
1078A LEU* 5.2 2.7 - - + -
1080A LYS* 3.7 32.8 - - + -
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Residues in contact with GLY1035 (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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926A GLU* 4.2 29.3 - - - +
927A LYS 4.6 0.6 + - - -
961A GLU* 3.5 18.7 - - - +
1033A SER* 3.2 10.6 + - - -
1034A PHE* 1.3 79.3 - - - +
1036A TRP* 1.3 57.8 + - - +
1037A VAL 3.0 5.8 + - - -
1038A ARG* 3.5 14.4 + - - +
1039A GLN 4.4 1.0 + - - -
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Residues in contact with TRP1036 (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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958A LEU* 3.7 21.1 - - + -
961A GLU* 3.4 33.5 + - + +
962A ALA 3.6 9.6 + - - +
963A VAL* 3.3 41.8 + - + +
995A ILE* 6.1 0.2 - - + -
1001A LEU* 3.5 28.7 - - + -
1032A LEU* 4.5 0.8 - - + +
1033A SER 3.2 28.2 + - - -
1035A GLY* 1.3 74.5 - - - +
1037A VAL* 1.3 69.1 + - + +
1038A ARG 3.1 0.4 - - - -
1039A GLN* 2.9 20.7 + - + +
1040A ILE* 4.1 13.6 + - + -
1045A VAL* 3.6 33.4 - - + -
1047A VAL* 4.9 7.2 - - + -
1078A LEU* 3.5 29.5 - - + +
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Residues in contact with VAL1037 (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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923A GLU* 4.6 12.1 - - - +
1034A PHE* 3.1 28.9 - - + +
1035A GLY 3.0 0.6 + - - -
1036A TRP* 1.3 90.9 - - + +
1038A ARG* 1.3 60.3 - - - +
1040A ILE* 3.7 16.7 - - - +
1041A LEU 4.2 0.5 + - - -
1042A GLN 4.1 14.3 - - - +
1043A LYS* 4.5 20.3 + - + +
1045A VAL* 4.8 9.4 - - + +
1078A LEU* 3.7 42.8 - - + +
1080A LYS 5.4 2.0 - - - +
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Residues in contact with ARG1038 (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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926A GLU* 4.5 15.5 - - - +
1034A PHE 4.7 0.2 + - - -
1035A GLY 3.5 9.4 + - - +
1036A TRP 3.1 0.6 - - - -
1037A VAL* 1.3 75.6 - - - +
1039A GLN* 1.3 67.4 + - - +
1040A ILE 2.8 7.9 + - - -
1041A LEU* 2.9 22.1 + - + +
1043A LYS* 5.6 6.5 - - - +
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Residues in contact with GLN1039 (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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958A LEU* 4.6 17.7 - - + +
959A ASN* 3.4 28.9 + - + +
961A GLU* 4.2 21.5 + - + +
991A PHE* 4.8 15.8 - - + -
1035A GLY 4.4 1.2 + - - -
1036A TRP* 2.9 23.8 + - + +
1038A ARG* 1.3 83.1 - - - +
1040A ILE* 1.3 65.5 + - + +
1041A LEU* 5.3 0.5 - - - +
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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