Contacts of the helix formed by residues 1077 - 1089 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1037B VAL 3.8 2.2 - - - -
1038B GLN 3.2 24.9 - - - +
1039B ASP 3.9 9.2 - - - +
1040B GLN* 3.7 36.1 - - + -
1043B ASN* 3.9 13.3 - - + +
1075B HIS* 2.9 18.3 + + + -
1076B LYS* 1.3 112.5 - - + +
1078B ALA* 1.3 64.6 + - - +
1079B SER 3.2 2.6 + - - -
1080B ASN* 3.2 22.1 + - - +
1081B VAL 4.0 0.9 + - - -
15D U 3.2 35.7 - + - -
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Residues in contact with ALA1078 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037B VAL* 3.1 26.4 + - + +
1038B GLN* 4.4 1.1 - - + -
1072B LEU* 3.6 36.3 - - + +
1075B HIS* 3.0 20.0 + - + +
1077B PHE* 1.3 75.8 - - - +
1079B SER* 1.3 65.2 + - - +
1081B VAL* 3.0 8.1 + - - +
1082B VAL* 3.0 22.5 + - - +
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Residues in contact with SER1079 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072B LEU 3.4 6.8 + - - -
1073B SER* 3.3 23.3 - - - +
1075B HIS 2.8 23.6 + - - -
1076B LYS 3.2 9.4 + - - -
1078B ALA* 1.3 77.5 - - - +
1080B ASN* 1.3 62.7 + - - +
1082B VAL* 3.2 8.3 + - - +
1083B GLU* 3.1 26.5 + - - +
1120B TYR* 3.8 10.1 - - - +
1124B VAL* 3.7 3.0 - - - +
14D G 2.9 24.0 + - - -
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Residues in contact with ASN1080 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047B GLN* 3.6 15.6 + - - +
1076B LYS 3.1 24.6 - - - +
1077B PHE 3.2 7.6 - - - +
1078B ALA 3.2 0.6 - - - -
1079B SER* 1.3 76.5 + - - +
1081B VAL* 1.3 62.9 + - - +
1083B GLU* 3.4 10.5 + - - +
1084B LYS* 3.2 31.5 + - - +
14D G 3.7 31.3 + - - +
15D U 3.0 50.5 + - - +
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Residues in contact with VAL1081 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037B VAL* 4.1 24.2 - - + +
1043B ASN* 3.7 39.3 - - + +
1046B ILE* 3.9 16.4 - - + -
1047B GLN* 3.8 10.1 - - + -
1050B LEU* 3.6 18.6 - - + +
1061B ILE* 4.4 0.4 - - + -
1065B ILE* 4.3 8.5 - - + -
1077B PHE 4.4 0.7 - - - +
1078B ALA* 3.0 10.7 + - + +
1080B ASN* 1.3 75.4 - - - +
1082B VAL* 1.3 60.4 + - - +
1084B LYS* 3.2 1.5 + - - +
1085B CYS* 2.8 35.2 + - - -
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Residues in contact with VAL1082 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065B ILE* 4.5 18.6 - - + -
1069B VAL* 3.9 14.6 - - + +
1072B LEU* 3.6 27.8 - - + -
1073B SER* 3.7 15.5 - - - +
1078B ALA 3.0 18.2 + - - +
1079B SER 3.2 6.9 + - - +
1081B VAL* 1.3 76.6 - - + +
1083B GLU* 1.3 56.9 + - - +
1085B CYS* 3.1 9.4 + - - +
1086B VAL* 2.9 37.6 + - + +
1097B LEU* 6.5 0.4 - - + -
1124B VAL* 3.7 29.6 - - + -
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Residues in contact with GLU1083 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1079B SER 3.1 17.6 + - - +
1080B ASN* 3.5 11.4 - - - +
1082B VAL* 1.3 76.3 - - - +
1084B LYS* 1.3 65.9 + - - +
1086B VAL* 2.9 11.7 + - - +
1087B THR* 2.8 32.1 + - - -
1123B TYR* 3.1 14.4 - - - +
1124B VAL* 4.1 14.4 - - + -
1127B LYS* 2.7 48.7 + - + +
14D G 2.7 44.0 + - - +
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Residues in contact with LYS1084 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047B GLN* 3.0 32.3 + - + +
1050B LEU* 3.4 28.8 - - + +
1051B GLU* 3.2 41.3 - - + +
1080B ASN* 3.2 19.1 + - - +
1081B VAL 3.2 2.7 + - - +
1083B GLU* 1.3 91.6 + - + +
1085B CYS* 1.3 56.7 + - - +
1087B THR* 4.4 4.7 - - - +
1088B HIS* 2.8 41.7 + - + +
1127B LYS* 5.1 7.0 - - - +
15D U 5.3 0.6 + - - -
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Residues in contact with CYS1085 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050B LEU* 3.8 17.5 - - - -
1061B ILE* 3.9 11.0 - - - -
1062B VAL* 3.9 26.7 - - + -
1065B ILE* 3.6 28.7 - - + -
1081B VAL* 2.8 18.9 + - - -
1082B VAL* 3.3 11.2 - - - +
1084B LYS* 1.3 76.5 - - - +
1086B VAL* 1.3 60.9 + - - +
1089B ALA* 2.9 32.8 + - - +
1097B LEU* 4.1 12.8 - - + +
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Residues in contact with VAL1086 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082B VAL* 2.9 28.7 + - + +
1083B GLU* 2.9 10.5 + - - +
1085B CYS* 1.3 78.1 - - - +
1087B THR* 1.3 60.1 + - - +
1089B ALA* 4.3 0.4 + - - -
1094B ARG* 3.4 24.9 + - + +
1097B LEU* 4.7 14.4 - - + -
1098B ILE* 4.9 4.0 - - + -
1124B VAL* 4.6 2.7 - - + +
1127B LYS* 3.8 16.8 - - + +
1128B MET* 3.8 41.3 - - + -
1131B VAL* 3.4 25.8 - - + +
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Residues in contact with THR1087 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083B GLU 2.8 15.7 + - - -
1084B LYS* 4.1 3.4 - - - -
1086B VAL* 1.3 81.1 - - - +
1088B HIS* 1.3 81.4 + - + +
1089B ALA 3.5 1.6 + - - +
1094B ARG* 4.0 8.7 + - - -
1127B LYS* 3.8 27.0 + - - +
1131B VAL* 4.0 20.7 - - + +
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Residues in contact with HIS1088 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050B LEU* 2.5 37.1 + - + +
1051B GLU* 3.1 45.6 + - + +
1058B LYS* 2.7 41.2 + - + +
1084B LYS* 2.8 26.3 + - - +
1085B CYS* 4.0 2.2 - - - -
1087B THR* 1.3 99.4 - - + +
1089B ALA* 1.3 60.5 + - - +
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Residues in contact with ALA1089 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058B LYS* 5.3 0.7 - - - +
1062B VAL* 4.1 12.1 - - + -
1085B CYS 2.9 20.9 + - - +
1086B VAL 4.3 1.2 + - - +
1087B THR 3.5 3.1 - - - +
1088B HIS* 1.3 81.1 - - - +
1090B SER* 1.3 68.7 + - - +
1093B GLU* 3.3 28.5 - - + +
1094B ARG* 3.4 24.1 + - - +
1097B LEU* 4.6 2.7 - - + -
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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