Contacts of the helix formed by residues 1118 - 1127 (chain U) in PDB entry 6FF7
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 SER1118 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064U ALA 3.7 16.2 - - - -
1065U ALA* 3.9 21.8 - - - -
1066U GLN 5.2 0.2 - - - -
1067U ILE 3.0 26.2 - - - -
1069U GLU* 4.2 2.7 - - - +
1101U PRO* 5.9 0.6 - - - +
1102U PRO 5.8 0.4 - - - -
1116U GLU 3.1 6.8 + - - -
1117U GLN* 1.3 77.5 - - - +
1119U LEU* 1.3 64.2 + - - +
1120U PHE 3.2 3.4 - - - -
1121U THR* 3.4 11.8 + - - -
1122U ARG* 3.1 22.0 + - - +
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Residues in contact with LEU1119 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067U ILE 4.1 2.0 + - - -
1069U GLU* 3.8 18.9 - - + +
1072U THR* 3.7 27.3 - - - -
1073U PHE 5.5 0.4 - - - +
1118U SER* 1.3 70.7 - - - +
1120U PHE* 1.3 67.2 + - - +
1122U ARG* 3.2 7.8 + - - +
1123U PHE* 2.9 25.1 + - - +
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Residues in contact with PHE1120 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064U ALA* 3.6 41.4 + - + +
1065U ALA* 4.0 9.0 - - + +
1072U THR* 5.5 0.6 - - - -
1093U MET* 5.5 5.8 - - + -
1095U GLY* 6.0 1.3 - - - -
1097U HIS* 5.6 1.1 - - + -
1118U SER* 4.0 0.4 - - - -
1119U LEU* 1.3 79.7 - - - +
1121U THR* 1.3 62.2 + - - +
1123U PHE* 3.2 7.0 + - - +
1124U VAL* 3.1 21.7 + - - +
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Residues in contact with THR1121 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065U ALA* 5.2 2.2 - - - +
1097U HIS* 4.2 26.2 - - - +
1117U GLN* 5.1 5.8 - - - -
1118U SER* 3.4 21.9 + - - -
1119U LEU 3.3 0.4 - - - -
1120U PHE* 1.3 76.5 - - - +
1122U ARG* 1.3 65.9 + - - +
1124U VAL* 3.3 5.4 + - - +
1125U ARG* 3.0 23.7 + - - +
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Residues in contact with ARG1122 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456U ASN 4.2 18.2 - - - +
457U LEU* 5.5 7.9 - - - +
1117U GLN* 5.7 5.8 - - + +
1118U SER 3.1 14.7 + - - +
1119U LEU* 3.6 10.3 - - - +
1121U THR* 1.3 75.8 - - - +
1123U PHE* 1.3 52.1 + - - +
1125U ARG* 3.3 8.1 + - - +
1126U VAL* 2.8 35.6 + - - +
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Residues in contact with PHE1123 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119U LEU 2.9 17.0 + - - +
1120U PHE* 3.5 7.2 - - - +
1122U ARG* 1.3 74.7 - - - +
1124U VAL* 1.3 64.6 + - - +
1126U VAL* 3.3 7.2 + - - +
1127U GLY 3.0 5.5 + - - -
1128U VAL* 3.0 37.9 + - + +
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Residues in contact with VAL1124 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097U HIS* 5.4 8.5 - - + -
1120U PHE 3.1 12.6 + - - +
1121U THR* 3.6 10.3 - - - +
1123U PHE* 1.3 74.7 - - - +
1125U ARG* 1.3 63.5 + - - +
1127U GLY* 3.1 14.7 + - - -
1128U VAL 4.6 9.3 - - - +
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Residues in contact with ARG1125 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158U GLU* 5.8 3.3 - - - +
456U ASN 6.0 1.3 - - - +
457U LEU* 6.1 4.5 - - + -
1121U THR 3.0 13.6 + - - +
1122U ARG* 3.5 11.4 - - - +
1124U VAL* 1.3 76.9 - - - +
1126U VAL* 1.3 63.1 + - - +
1127U GLY* 3.3 0.9 + - - -
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Residues in contact with VAL1126 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457U LEU* 5.6 11.4 - - + +
690U ILE 5.7 2.5 - - - +
693U GLY* 4.9 20.4 - - - +
697U PRO* 3.9 14.3 - - + +
1122U ARG 2.8 21.2 + - - +
1123U PHE* 3.6 9.6 - - - +
1124U VAL 3.3 0.2 - - - -
1125U ARG* 1.3 73.4 - - - +
1127U GLY* 1.3 58.3 + - - +
1128U VAL* 4.8 1.8 - - + +
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Residues in contact with GLY1127 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697U PRO* 3.5 14.4 - - - +
698U SER* 5.0 2.1 + - - -
1123U PHE 3.0 2.8 + - - -
1124U VAL 3.1 11.5 + - - -
1125U ARG 3.1 1.5 - - - -
1126U VAL* 1.3 78.1 - - - +
1128U VAL* 1.3 68.5 + - - +
1129U PRO* 3.3 3.8 - - - +
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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