Contacts of the helix formed by residues 1072 - 1081 (chain A) in PDB entry 5M64
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 ASN1072 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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745A PRO* 6.4 0.4 - - - -
746A GLY 3.6 11.5 - - - +
747A ILE* 4.5 6.8 - - - +
748A ASN* 3.5 29.5 + - - +
749A LEU* 4.7 0.8 - - - +
800A VAL* 3.7 22.7 - - + +
1068A PHE* 3.0 33.1 + - + +
1069A CYS 3.3 3.8 - - - -
1071A ASP* 1.3 84.5 - - - +
1073A TYR* 1.3 65.2 + - - +
1074A TYR 3.5 1.8 - - - -
1075A ALA* 3.7 19.7 - - + -
1076A LEU* 3.1 28.9 + - + +
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Residues in contact with TYR1073 (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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1069A CYS 3.1 13.1 + - - +
1070A LEU* 3.1 20.9 - - - +
1071A ASP* 4.3 10.1 - - - -
1072A ASN* 1.3 76.4 - - - +
1074A TYR* 1.3 113.3 + + + +
1076A LEU* 4.0 0.4 - - - +
1077A LEU* 3.0 33.6 + - + +
1160A GLY 4.7 11.8 + - - -
1161A VAL* 4.4 35.9 - - + -
1166A PHE* 5.2 5.8 - - + -
1169A LEU* 4.0 13.9 - - + +
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Residues in contact with TYR1074 (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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745A PRO* 3.6 23.3 - - + +
1073A TYR* 1.3 117.0 - + + +
1075A ALA* 1.3 65.5 + - - +
1077A LEU* 3.9 25.3 - - + +
1078A LYS* 3.4 22.0 + - - +
1160A GLY 5.4 3.8 + - - -
1161A VAL* 5.7 2.2 - - + +
1165A LYS* 4.9 16.0 - - - -
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Residues in contact with ALA1075 (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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744A MET* 3.2 38.6 - - + +
745A PRO* 3.8 26.1 - - + +
746A GLY 4.6 2.0 - - - +
747A ILE* 6.2 1.1 - - + -
800A VAL* 5.0 6.7 - - + -
1072A ASN* 3.2 28.8 + - + +
1073A TYR 3.1 0.8 - - - -
1074A TYR* 1.3 81.4 - - - +
1076A LEU* 1.3 61.4 + - - +
1078A LYS* 3.6 5.5 + - - +
1079A LYS* 3.9 5.7 + - - +
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Residues in contact with LEU1076 (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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744A MET* 5.2 0.4 - - - -
799A GLU 5.6 0.2 - - - +
800A VAL* 5.4 8.7 - - + +
1068A PHE* 5.0 11.7 - - + -
1069A CYS* 3.8 29.6 - - + +
1072A ASN* 3.3 20.9 - - + +
1073A TYR 4.2 0.2 - - - +
1075A ALA* 1.3 77.2 - - - +
1077A LEU* 1.3 64.4 + - - +
1078A LYS 3.2 0.9 - - - -
1079A LYS* 3.3 15.5 - - - +
1080A TYR* 2.9 64.6 + - + -
1169A LEU* 3.7 35.2 - - + +
1173A LYS* 5.5 3.8 - - + -
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Residues in contact with LEU1077 (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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1073A TYR* 3.0 21.6 + - + +
1074A TYR* 4.0 29.4 - - + +
1076A LEU* 1.3 79.9 - - - +
1078A LYS* 1.3 61.0 + - - +
1080A TYR* 4.8 2.5 - - + -
1081A ASN* 3.2 18.7 + - - -
1082A PRO* 3.6 31.8 - - + +
1165A LYS* 5.1 21.3 - - + +
1169A LEU* 3.7 26.9 - - + -
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Residues in contact with LYS1078 (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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741A PRO* 5.5 2.4 - - - +
742A PRO 3.6 6.5 + - - -
743A ASP* 2.7 41.6 + - + +
744A MET* 3.4 29.4 - - - +
745A PRO* 5.4 1.3 - - + -
1074A TYR 3.4 15.3 + - - +
1075A ALA 4.0 1.8 - - - +
1076A LEU 3.2 0.8 - - - -
1077A LEU* 1.3 82.1 - - - +
1079A LYS* 1.3 61.8 + - - +
1081A ASN* 3.9 12.1 + - - +
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Residues in contact with LYS1079 (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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744A MET* 5.6 2.5 - - + -
799A GLU* 3.4 26.0 + - - +
800A VAL 4.5 12.1 - - - +
801A TYR 6.0 2.5 - - - +
1075A ALA 3.9 4.4 + - - +
1076A LEU* 3.3 23.5 - - - +
1078A LYS* 1.3 83.1 - - - +
1080A TYR* 1.3 109.6 + - + +
1081A ASN* 4.6 2.1 - - - +
1176A ARG* 5.4 3.1 + - - -
154F ASP 5.6 2.3 - - - +
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Residues in contact with TYR1080 (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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799A GLU* 6.1 1.0 - - - +
1076A LEU* 2.9 51.1 + - + +
1077A LEU* 4.4 3.8 - - - +
1079A LYS* 1.3 110.5 + - + +
1081A ASN* 1.3 71.3 + - - +
1082A PRO* 4.5 6.7 - - + -
1085A LEU* 5.3 0.3 - - - +
1169A LEU* 5.5 3.8 - - + +
1172A LEU* 3.7 27.2 - - + +
1173A LYS* 3.3 39.7 + - + +
1176A ARG* 3.9 53.3 + - + +
1177A SER* 5.5 1.2 + - - -
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Residues in contact with ASN1081 (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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1077A LEU 3.2 12.7 + - - -
1078A LYS 3.9 11.0 + - - +
1079A LYS 3.4 2.9 - - - +
1080A TYR* 1.3 80.1 - - - +
1082A PRO* 1.3 69.0 - - - +
1083A SER* 3.7 16.6 + - - -
1084A ALA* 3.3 34.9 + - + +
1085A LEU* 4.3 5.7 + - - +
1172A LEU* 4.8 0.2 - - - +
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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