Contacts of the helix formed by residues 1125 - 1133 (chain A) in PDB entry 6TPN
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 GLY1125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1122A GLU* 3.5 25.0 + - - +
1124A PHE* 1.3 78.4 - - - +
1126A LEU* 1.3 64.6 + - - +
1127A VAL 3.2 3.1 - - - -
1128A ALA 3.3 9.3 + - - -
1129A LEU* 3.4 5.6 + - - +
1145A GLY* 3.9 3.5 - - - -
1146A LEU* 3.9 16.4 - - - -
1149A ILE* 3.2 22.7 - - - +
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Residues in contact with LEU1126 (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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252A CYS 5.1 3.6 - - - +
253A ARG 4.0 21.1 - - - +
254A GLN* 4.3 12.1 - - - +
1001A GLY 5.0 6.7 - - - +
1002A ILE* 4.0 35.7 - - + +
1122A GLU* 4.6 3.6 + - - -
1124A PHE* 3.5 3.6 - - + +
1125A GLY* 1.3 78.2 - - - +
1127A VAL* 1.3 65.0 + - + +
1129A LEU* 3.4 10.0 + - + +
1130A GLU* 3.0 50.7 + - - +
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Residues in contact with VAL1127 (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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1038A ILE* 4.0 24.2 - - + +
1046A LYS* 5.9 6.3 - - - -
1109A TYR* 3.4 23.1 + - + +
1115A VAL* 4.9 3.8 - - + -
1117A ILE* 4.7 26.0 - - + -
1122A GLU* 4.9 11.9 - - - +
1125A GLY* 3.2 1.0 - - - -
1126A LEU* 1.3 81.1 - - + +
1128A ALA* 1.3 56.5 + - - +
1130A GLU* 3.3 11.3 + - - +
1131A ALA* 3.0 28.4 + - - +
1146A LEU* 5.9 0.7 - - + -
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Residues in contact with ALA1128 (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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1117A ILE* 4.4 11.8 - - + +
1125A GLY 3.3 10.5 + - - +
1126A LEU 3.3 0.4 - - - -
1127A VAL* 1.3 79.2 - - - +
1129A LEU* 1.3 57.4 + - - +
1131A ALA* 4.1 2.9 - - - +
1132A MET* 2.9 48.2 + - - +
1138A PRO* 5.1 2.0 - - + -
1146A LEU* 3.7 23.2 - - + +
1149A ILE* 4.4 8.5 - - + -
1150A ILE* 4.2 15.5 - - + -
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Residues in contact with LEU1129 (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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254A GLN* 4.7 6.1 - - + -
296A ILE* 3.9 25.6 - - + -
1002A ILE* 4.4 25.1 - - + -
1125A GLY 3.4 6.0 + - - +
1126A LEU* 3.8 15.3 - - + +
1127A VAL 3.4 0.2 - - - -
1128A ALA* 1.3 77.4 - - - +
1130A GLU* 1.3 62.1 + - - +
1133A CYS* 3.2 30.5 + - - -
1149A ILE* 3.8 22.9 - - + -
1192A ALA* 3.5 38.2 - - + +
1195A PHE* 3.7 23.1 - - + -
1196A SER* 4.1 4.0 - - - +
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Residues in contact with GLU1130 (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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1002A ILE* 3.7 22.5 - - + +
1007A TRP* 4.0 33.2 + - + -
1109A TYR* 3.9 24.4 + - + -
1126A LEU* 3.0 44.4 + - + +
1127A VAL* 3.6 15.8 - - - +
1129A LEU* 1.3 78.7 - - - +
1131A ALA* 1.3 60.6 + - - +
1133A CYS* 3.9 2.0 + - - +
1134A LEU* 3.3 27.0 - - - +
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Residues in contact with ALA1131 (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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1109A TYR* 3.7 28.0 - - + -
1115A VAL* 3.6 31.0 - - + -
1127A VAL 3.0 17.5 + - - +
1128A ALA* 4.1 2.5 - - - +
1130A GLU* 1.3 77.6 - - - +
1132A MET* 1.3 65.8 + - + +
1134A LEU* 3.1 10.7 + - - +
1136A ALA* 3.0 26.3 + - + +
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Residues in contact with MET1132 (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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1128A ALA 2.9 22.0 + - - +
1131A ALA* 1.3 76.1 - - - +
1133A CYS* 1.3 63.0 + - - +
1134A LEU 3.2 1.0 + - - -
1135A GLY 3.2 8.3 + - - -
1136A ALA 3.6 10.8 - - - +
1138A PRO* 3.6 33.0 - - + -
1149A ILE* 3.8 25.4 - - + +
1150A ILE* 4.2 6.5 - - - -
1154A THR* 4.0 14.4 - - - +
1188A CYS* 3.5 32.1 - - + +
1189A LYS* 3.4 19.4 + - - +
1191A ARG* 3.8 26.7 - - + -
1192A ALA* 3.7 10.3 - - + +
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Residues in contact with CYS1133 (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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1002A ILE* 5.1 8.5 - - - -
1004A YCM 3.6 24.5 - - - -
1007A TRP* 3.9 20.6 - - + +
1008A ASN* 5.1 0.3 - - - -
1009A GLU* 3.4 25.5 + - - +
1129A LEU 3.2 25.1 + - - +
1130A GLU 4.0 5.6 - - - +
1131A ALA 3.2 0.2 - - - -
1132A MET* 1.3 76.3 - - - +
1134A LEU* 1.3 61.7 + - + +
1135A GLY 3.5 0.2 - - - -
1189A LYS* 3.9 10.0 - - - +
1192A ALA* 3.6 22.2 - - - -
1193A MET* 4.5 8.0 - - + +
1196A SER* 4.9 4.3 - - - -
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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