Contacts of the helix formed by residues 1069 - 1083 (chain B) in PDB entry 1G24
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 SER1069 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1067B GLY 3.6 2.1 + - - -
1068B LEU* 1.3 76.7 - - - +
1070B LYS* 1.3 64.0 + - - +
1071B SER* 3.0 23.6 + - - -
1072B GLU* 2.9 28.5 + - - +
1073B LYS* 3.0 23.0 + - - +
1117B LYS* 4.5 4.5 - - - -
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Residues in contact with LYS1070 (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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1069B SER* 1.3 73.5 - - - +
1071B SER* 1.3 57.6 + - - +
1073B LYS* 3.3 10.6 + - + +
1074B GLU* 2.9 56.6 + - + +
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Residues in contact with SER1071 (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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1069B SER* 3.0 15.1 + - - -
1070B LYS* 1.3 80.2 - - - +
1072B GLU* 1.3 59.8 + - - +
1074B GLU* 3.5 13.5 + - - +
1075B ALA* 3.0 22.7 + - - +
1106B LYS* 4.9 7.2 - - - -
1110B LEU* 3.8 30.1 - - - +
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Residues in contact with GLU1072 (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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1068B LEU* 3.4 11.8 - - + +
1069B SER* 2.9 40.4 + - - +
1071B SER* 1.3 73.0 - - - +
1073B LYS* 1.3 66.5 + - - +
1075B ALA* 3.2 8.1 + - - +
1076B ILE* 3.0 27.8 + - - +
1110B LEU* 4.3 20.6 - - + +
1111B LEU* 4.8 0.3 - - - +
1113B LYS* 4.4 12.3 - - - +
1114B SER* 3.7 38.9 + - - -
1117B LYS* 2.9 27.1 + - - +
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Residues in contact with LYS1073 (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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1063B TYR* 2.9 33.9 + - - +
1068B LEU* 3.9 35.0 - - + +
1069B SER 3.0 17.2 + - - +
1070B LYS* 3.3 10.5 + - - +
1072B GLU* 1.3 77.4 - - - +
1074B GLU* 1.3 57.5 + - + +
1076B ILE* 3.0 7.4 + - - +
1077B VAL* 2.8 33.4 + - + +
1206B ILE* 3.9 20.7 - - + +
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Residues in contact with GLU1074 (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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1070B LYS* 2.9 50.2 + - + +
1071B SER* 3.8 12.2 - - - +
1072B GLU 3.3 0.2 - - - -
1073B LYS* 1.3 77.4 - - + +
1075B ALA* 1.3 57.7 + - - +
1077B VAL* 3.2 9.1 + - - +
1078B SER* 2.8 34.9 + - - +
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Residues in contact with ALA1075 (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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1071B SER 3.0 14.8 + - - +
1072B GLU 3.5 8.7 - - - +
1073B LYS 3.2 0.2 - - - -
1074B GLU* 1.3 76.6 - - - +
1076B ILE* 1.3 57.1 + - - +
1078B SER* 3.4 7.7 + - - -
1079B TYR* 2.9 23.4 + - - +
1107B GLN* 3.8 27.8 - - + +
1110B LEU* 3.8 17.0 - - + -
1111B LEU* 3.4 24.3 - - + +
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Residues in contact with ILE1076 (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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1068B LEU* 3.9 16.2 - - + -
1072B GLU 3.0 20.3 + - - +
1073B LYS* 3.4 7.4 - - - +
1075B ALA* 1.3 73.9 - - - +
1077B VAL* 1.3 66.9 + - - +
1079B TYR* 3.1 5.0 + - + +
1080B THR* 3.0 23.7 + - + +
1111B LEU* 3.6 18.8 - - + -
1114B SER* 4.5 6.7 - - - +
1118B MET* 4.4 14.4 - - + -
1203B ILE* 3.7 43.3 - - + +
1206B ILE* 3.8 32.3 - - + -
1207B SER* 5.2 0.9 - - - -
1216B LEU* 5.5 4.9 - - + -
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Residues in contact with VAL1077 (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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1073B LYS* 2.8 21.8 + - + +
1074B GLU* 3.6 10.1 - - - +
1076B ILE* 1.3 76.9 - - - +
1078B SER* 1.3 63.1 + - - +
1080B THR* 2.6 24.8 + - - -
1081B LYS* 3.1 38.5 + - + +
1206B ILE* 3.6 25.1 - - + +
1207B SER* 4.0 13.9 - - - +
1209B PHE* 5.7 0.2 - - + -
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Residues in contact with SER1078 (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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1074B GLU* 2.8 20.0 + - - +
1075B ALA* 3.6 6.3 - - - -
1077B VAL* 1.3 77.2 - - - +
1079B TYR* 1.3 63.5 + - - +
1081B LYS* 3.2 10.6 + - - +
1082B SER* 3.1 25.5 + - - -
1086B ILE* 4.3 3.0 - - - +
1107B GLN* 3.4 35.6 + - - -
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Residues in contact with TYR1079 (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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1075B ALA 2.9 14.6 + - - +
1076B ILE* 3.1 8.9 + - - +
1078B SER* 1.3 77.2 - - - +
1080B THR* 1.3 68.9 + - + +
1083B ALA* 2.8 52.8 + - + +
1086B ILE* 3.9 21.7 - - + +
1087B ASN* 3.2 28.1 + - - -
1111B LEU* 4.1 13.9 - - + -
1172B TYR* 3.7 37.6 + + + +
1174B SER* 2.9 29.4 + - - -
1203B ILE* 4.8 1.8 - - + -
1214B GLU* 4.1 5.6 - - - -
1216B LEU* 3.6 31.2 - - + +
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Residues in contact with THR1080 (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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1076B ILE* 3.0 12.8 + - + +
1077B VAL 2.6 18.4 + - - -
1079B TYR* 1.3 83.2 - - + +
1081B LYS* 1.3 59.3 + - - +
1083B ALA* 4.3 7.5 + - - +
1203B ILE* 4.0 21.8 - - + -
1207B SER* 2.7 33.3 + - - -
1209B PHE* 3.9 26.2 - - - +
1210B ALA* 3.9 14.4 - - - -
1214B GLU* 4.7 2.5 - - - +
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Residues in contact with LYS1081 (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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1077B VAL* 3.1 34.7 + - + +
1078B SER* 3.7 10.1 - - - +
1079B TYR 3.1 1.2 - - - -
1080B THR* 1.3 80.0 + - - +
1082B SER* 1.3 63.4 + - - +
1083B ALA 3.8 0.2 - - - -
1209B PHE* 3.7 39.2 - - + -
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Residues in contact with SER1082 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078B SER 3.1 13.7 + - - -
1079B TYR 3.5 2.0 - - - -
1081B LYS* 1.3 85.4 + - - +
1083B ALA* 1.3 64.0 + - - +
1084B SER 3.4 2.7 - - - -
1085B GLU* 3.1 20.5 + - - +
1086B ILE* 2.9 33.3 + - - +
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Residues in contact with ALA1083 (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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1079B TYR* 2.8 52.7 + - + +
1080B THR* 4.3 7.3 + - - +
1081B LYS 3.8 1.0 - - - -
1082B SER* 1.3 72.2 - - - +
1084B SER* 1.3 58.3 + - - +
1086B ILE* 4.6 0.2 - - - -
1087B ASN* 2.8 39.0 + - - +
1174B SER* 5.4 0.9 - - - +
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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