Contacts of the helix formed by residues 1077 - 1089 (chain A) in PDB entry 1M8X
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 PHE1077 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1037A VAL 3.6 7.0 - - - +
1038A GLN 3.6 21.8 - - - +
1039A ASP 4.1 2.2 - - - -
1040A GLN* 3.8 33.7 - - + -
1043A ASN* 3.7 20.1 - - - +
1075A HIS* 3.0 20.2 + + + +
1076A LYS* 1.3 102.6 - - + +
1078A ALA* 1.3 63.7 + - - +
1079A SER 3.1 2.8 + - - -
1080A ASN* 3.3 21.4 + - - +
1081A VAL 3.9 1.4 + - - -
15C U 3.1 48.9 - + - -
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Residues in contact with ALA1078 (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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1037A VAL* 3.2 29.3 + - + +
1038A GLN* 4.1 1.1 - - + -
1065A ILE* 5.9 0.2 - - - +
1072A LEU* 3.7 40.3 - - + +
1075A HIS* 3.1 14.6 + - + +
1077A PHE* 1.3 74.1 - - - +
1079A SER* 1.3 65.2 + - - +
1081A VAL* 2.8 16.4 + - - +
1082A VAL* 2.9 14.0 + - - +
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Residues in contact with SER1079 (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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1072A LEU 3.3 8.3 + - - -
1073A SER* 3.3 21.8 - - - +
1075A HIS 2.8 24.2 + - - -
1076A LYS 3.3 10.2 + - - -
1078A ALA* 1.3 76.7 - - - +
1080A ASN* 1.3 62.4 + - - +
1082A VAL* 3.1 19.2 + - - +
1083A GLU* 3.1 16.3 + - - +
1120A TYR* 3.9 8.9 - - - +
1124A VAL* 3.9 2.6 - - - +
14C G 2.8 27.6 + - - -
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Residues in contact with ASN1080 (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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1047A GLN* 3.8 10.1 - - - +
1076A LYS 3.2 25.1 + - - -
1077A PHE 3.4 11.1 + - - +
1079A SER* 1.3 78.0 + - - +
1081A VAL* 1.3 60.9 + - - +
1083A GLU* 3.4 9.2 + - - +
1084A LYS* 3.2 31.6 + - - +
14C G 3.1 32.2 + - - +
15C U 3.2 52.2 - - + +
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Residues in contact with VAL1081 (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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1037A VAL* 3.9 35.4 - - + +
1043A ASN* 3.8 40.6 - - + +
1046A ILE* 4.0 17.0 - - + -
1047A GLN* 4.1 9.9 - - + +
1050A LEU* 4.0 9.6 - - + -
1061A ILE* 4.7 0.4 - - + -
1065A ILE* 4.2 12.1 - - + -
1077A PHE 4.2 1.1 - - - +
1078A ALA* 2.8 12.4 + - - +
1080A ASN* 1.3 75.6 - - - +
1082A VAL* 1.3 64.3 + - - +
1084A LYS* 3.3 3.2 + - - +
1085A CYS* 3.1 20.6 + - - -
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Residues in contact with VAL1082 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065A ILE* 4.3 18.6 - - + +
1069A VAL* 4.4 17.7 - - + +
1072A LEU* 4.0 7.9 - - + -
1073A SER* 3.7 21.5 - - - +
1078A ALA 2.9 16.9 + - - +
1079A SER* 3.2 16.4 - - - +
1081A VAL* 1.3 72.6 - - - +
1083A GLU* 1.3 66.3 + - - +
1085A CYS* 3.2 10.1 + - + +
1086A VAL* 2.9 27.3 + - + +
1097A LEU* 6.2 1.3 - - + -
1124A VAL* 3.6 26.9 - - + -
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Residues in contact with GLU1083 (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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1079A SER 3.1 14.1 + - - +
1080A ASN* 3.5 12.3 - - - +
1082A VAL* 1.3 78.0 - - - +
1084A LYS* 1.3 74.3 + - + +
1086A VAL* 2.9 11.3 + - - +
1087A THR* 2.9 25.7 + - - -
1123A TYR* 3.5 14.6 - - - +
1124A VAL* 4.0 20.0 - - + -
1127A LYS* 3.8 28.6 + - + +
14C G 2.6 46.4 + - - +
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Residues in contact with LYS1084 (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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1047A GLN* 3.1 41.3 + - + +
1050A LEU* 3.6 23.0 - - + +
1051A GLU* 3.2 37.9 - - + -
1080A ASN* 3.2 14.8 + - - +
1081A VAL 3.7 3.6 - - - +
1082A VAL 3.3 0.4 - - - -
1083A GLU* 1.3 88.1 + - + +
1085A CYS* 1.3 58.3 + - - +
1087A THR* 4.5 2.2 - - - -
1088A HIS* 2.9 41.1 + - + +
15C U 5.1 1.6 + - - -
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Residues in contact with CYS1085 (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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1050A LEU* 3.7 21.3 - - - -
1061A ILE* 4.3 2.9 - - - -
1062A VAL* 4.1 19.1 - - + -
1065A ILE* 3.4 34.8 - - + -
1081A VAL* 3.1 21.3 + - - -
1082A VAL* 3.4 9.6 - - - +
1083A GLU 3.1 0.6 - - - -
1084A LYS* 1.3 74.7 - - - +
1086A VAL* 1.3 62.9 + - - +
1089A ALA* 2.8 35.7 + - - +
1097A LEU* 4.0 16.8 - - + -
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Residues in contact with VAL1086 (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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1082A VAL* 2.9 26.2 + - + +
1083A GLU* 2.9 11.4 + - - +
1085A CYS* 1.3 78.4 - - - +
1087A THR* 1.3 56.6 + - - +
1094A ARG* 3.2 34.9 + - + +
1097A LEU* 4.3 16.2 - - + -
1098A ILE* 5.4 2.7 - - + -
1124A VAL* 4.8 1.8 - - + -
1127A LYS* 3.9 18.8 - - + +
1128A MET* 4.0 35.9 - - + -
1131A VAL* 3.2 27.9 - - + +
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Residues in contact with THR1087 (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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1083A GLU 2.9 10.7 + - - -
1084A LYS* 3.9 2.9 - - - +
1086A VAL* 1.3 78.5 - - - +
1088A HIS* 1.3 87.0 + - + +
1089A ALA 3.6 0.4 - - - +
1094A ARG* 3.9 8.3 + - - -
1127A LYS* 3.3 32.3 + - - +
1131A VAL* 4.1 14.8 - - + +
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Residues in contact with HIS1088 (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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1050A LEU* 3.2 31.8 + - + +
1051A GLU* 3.9 37.9 + - + +
1058A LYS* 4.0 26.4 + - + +
1084A LYS* 2.9 36.1 + - + +
1085A CYS* 3.8 0.4 - - - -
1087A THR* 1.3 94.9 + - + +
1089A ALA* 1.3 67.5 + - - +
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Residues in contact with ALA1089 (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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1058A LYS* 6.0 1.3 - - - -
1062A VAL* 4.2 12.3 - - + -
1085A CYS* 2.8 21.6 + - - +
1086A VAL 4.1 0.4 + - - -
1087A THR 3.6 1.6 - - - +
1088A HIS* 1.3 83.5 - - - +
1090A SER* 1.3 68.5 + - - +
1093A GLU* 3.3 29.4 - - + +
1094A ARG* 3.1 25.8 + - + +
1097A LEU* 4.4 3.4 - - + -
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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