Contacts of the helix formed by residues 1073 - 1082 (chain B) in PDB entry 5TWV
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 SER1073 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030B ILE* 4.7 1.3 - - - +
1069B THR 5.3 1.1 - - - -
1070B LEU* 3.7 16.1 + - - -
1071B LEU 3.6 2.4 - - - -
1072B CYS* 1.3 79.3 - - - +
1074B LEU* 1.3 60.4 + - - +
1075B GLY 3.2 6.0 + - - -
1076B ILE* 4.3 2.3 + - - +
1077B VAL* 3.9 12.5 + - - +
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Residues in contact with LEU1074 (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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1023B LYS* 4.7 5.2 - - + +
1026B VAL* 3.8 28.7 - - + +
1027B LEU* 4.9 1.1 - - - +
1030B ILE* 3.8 24.5 - - + +
1073B SER* 1.3 75.4 - - - +
1075B GLY* 1.3 57.9 + - - +
1077B VAL* 3.8 13.9 - - + -
1078B LEU* 2.8 31.5 - - - +
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Residues in contact with GLY1075 (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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551B PRO* 3.7 19.3 - - - +
554B ALA* 6.0 3.8 - - - -
1030B ILE* 4.5 3.8 - - - +
1072B CYS* 4.1 9.2 + - - -
1073B SER 3.2 4.6 - - - -
1074B LEU* 1.3 75.7 - - - +
1076B ILE* 1.3 62.6 + - - +
1078B LEU* 3.8 1.0 - - - +
1079B CYS* 2.9 28.1 + - - +
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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
----------------------------------------------------------
551B PRO* 5.7 0.2 - - - -
1072B CYS 5.2 1.0 + - - -
1073B SER 4.3 3.4 + - - +
1075B GLY* 1.3 75.0 - - - +
1077B VAL* 1.3 57.2 + - - +
1079B CYS* 3.7 7.8 - - + +
1080B LEU* 2.9 33.1 + - + +
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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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1023B LYS* 5.0 2.9 - - + -
1073B SER 3.9 7.4 + - - +
1074B LEU* 3.8 20.4 - - + -
1075B GLY 3.2 0.4 - - - +
1076B ILE* 1.3 77.6 - - - +
1078B LEU* 1.3 59.3 + - - +
1080B LEU* 5.0 1.6 - - - -
1081B VAL* 2.9 42.5 + - + +
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Residues in contact with LEU1078 (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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551B PRO* 5.1 4.5 - - + -
1023B LYS* 4.1 29.4 - - + +
1024B HIS* 5.8 0.7 - - - -
1027B LEU* 5.2 8.1 - - + -
1074B LEU* 2.8 25.1 + - + +
1075B GLY* 3.8 3.6 - - - +
1077B VAL* 1.3 77.2 - - - +
1079B CYS* 1.3 56.7 + - - +
1082B THR* 2.6 38.5 + - - -
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Residues in contact with CYS1079 (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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544B ILE* 4.7 4.5 - - - +
547B ASN* 4.5 8.9 - - - +
548B THR* 3.7 23.7 - - - +
551B PRO* 3.7 21.7 - - + +
1075B GLY 2.9 17.7 + - - +
1076B ILE* 3.7 10.3 - - + +
1077B VAL 3.3 0.2 - - - -
1078B LEU* 1.3 78.0 - - - +
1080B LEU* 1.3 59.7 + - - +
1082B THR* 5.0 0.2 - - - -
1083B SER* 3.6 20.3 + - - -
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Residues in contact with LEU1080 (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* 2.9 20.2 + - + +
1077B VAL* 4.4 2.0 - - - +
1079B CYS* 1.3 76.6 - - - +
1081B VAL* 1.3 62.9 + - + +
1082B THR 3.4 0.2 - - - -
1083B SER* 3.4 3.3 + - - -
1084B VAL* 3.0 27.8 + - - +
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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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1016B LEU 4.5 2.8 - - - +
1019B SER* 3.3 44.0 - - - +
1020B GLN* 3.9 8.2 - - - +
1023B LYS* 4.1 6.5 - - + -
1077B VAL* 2.9 27.7 + - + +
1080B LEU* 1.3 75.6 - - + +
1082B THR* 1.3 64.1 + - - +
1084B VAL* 3.1 22.2 + - + +
1085B THR 4.2 2.1 + - - -
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Residues in contact with THR1082 (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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547B ASN* 5.8 3.8 - - - -
1020B GLN* 3.8 25.8 - - - +
1023B LYS* 4.9 1.5 - - - +
1024B HIS* 6.3 0.4 - - - -
1078B LEU* 2.6 27.7 + - - +
1079B CYS* 4.9 0.7 - - - -
1081B VAL* 1.3 79.4 - - - +
1083B SER* 1.3 57.0 + - - +
1084B VAL 3.4 0.6 + - - -
1085B THR* 4.7 4.7 + - - -
1086B VAL 5.7 0.2 + - - -
1141B GLU* 5.4 8.3 - - - +
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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