Contacts of the helix formed by residues 1121 - 1131 (chain A) in PDB entry 4E5W
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 PRO1121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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977A LEU* 3.7 31.2 - - + -
1119A ASN 3.6 8.9 - - - +
1120A CYS* 1.4 90.2 - - - +
1122A ASP* 1.3 65.2 + - - +
1123A GLU* 3.6 27.8 - - + +
1124A VAL* 3.0 24.7 + - + -
1125A TYR* 3.1 10.2 + - - +
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Residues in contact with ASP1122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1116A CYS* 5.3 2.3 - - - -
1120A CYS 3.7 2.2 + - - -
1121A PRO* 1.3 70.7 - - - +
1123A GLU* 1.3 57.8 + - - +
1125A TYR* 3.2 13.0 + - - -
1126A GLN* 2.8 68.5 + - - +
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Residues in contact with GLU1123 (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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1121A PRO* 3.6 24.9 - - + +
1122A ASP* 1.3 81.4 + - - +
1124A VAL* 1.4 65.9 + - + +
1126A GLN* 3.8 7.1 + - - +
1127A LEU* 3.6 23.7 + - - +
1152A LEU* 3.7 31.9 - - + +
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Residues in contact with VAL1124 (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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977A LEU* 4.5 3.6 - - + -
981A LEU* 3.9 32.5 - - + -
1071A LEU* 4.7 4.1 - - + +
1075A LEU* 3.9 19.3 - - + -
1120A CYS* 3.7 16.4 - - - -
1121A PRO* 3.0 30.2 + - + +
1123A GLU* 1.4 75.0 - - + +
1125A TYR* 1.3 64.7 + - - +
1127A LEU* 3.1 16.5 + - - +
1128A MET* 3.2 11.3 + - - +
1149A PHE* 4.7 8.7 - - + -
1152A LEU* 3.9 21.3 - - + -
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Residues in contact with TYR1125 (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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1113A ARG 5.0 0.3 + - - -
1114A LEU 2.7 25.8 + - - -
1115A PRO* 3.8 3.3 - - - +
1116A CYS* 3.6 57.9 + - + -
1117A PRO* 4.3 1.6 - - + -
1120A CYS* 3.9 4.6 - - - -
1121A PRO 3.1 8.3 + - - +
1122A ASP* 3.6 13.2 - - - +
1124A VAL* 1.3 77.4 - - - +
1126A GLN* 1.3 68.3 + - - +
1128A MET* 3.2 29.5 + - - +
1129A ARG* 2.8 68.7 + - + +
1132A TRP* 4.3 2.5 - + - -
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Residues in contact with GLN1126 (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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1122A ASP* 2.8 51.4 + - - +
1123A GLU* 4.1 7.6 - - - +
1124A VAL 3.3 0.2 - - - -
1125A TYR* 1.3 85.4 - - - +
1127A LEU* 1.3 61.8 + - - +
1129A ARG* 3.4 20.9 + - - +
1130A LYS* 3.2 31.7 + - - +
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Residues in contact with LEU1127 (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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1071A LEU* 5.2 0.2 - - - -
1123A GLU 3.6 7.5 + - - +
1124A VAL 3.1 9.2 + - - +
1126A GLN* 1.3 74.2 - - - +
1128A MET* 1.3 66.3 + - - +
1130A LYS* 3.3 33.5 + - + +
1131A CYS* 3.6 11.3 + - - -
1140A THR* 5.7 0.2 - - - +
1144A ASN* 4.8 6.3 - - - +
1145A LEU* 3.8 28.8 - - + +
1148A GLY* 3.8 37.9 - - - +
1149A PHE* 3.9 27.4 - - + +
1152A LEU* 3.9 17.7 - - + -
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Residues in contact with MET1128 (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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1068A GLY 3.6 12.8 - - - +
1071A LEU* 4.0 15.8 - - + +
1072A HIS* 3.8 31.2 - - - +
1075A LEU* 3.5 32.1 - - + -
1117A PRO* 4.1 10.5 - - + -
1120A CYS* 4.9 0.4 - - - -
1124A VAL 3.2 9.5 + - - +
1125A TYR* 3.3 28.7 - - + +
1127A LEU* 1.3 76.1 - - - +
1129A ARG* 1.4 56.3 + - - +
1131A CYS* 3.1 29.5 + - - +
1132A TRP* 3.4 39.2 - - + -
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Residues in contact with ARG1129 (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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1111A GLY 4.3 9.7 + - - -
1113A ARG* 3.9 30.1 - - - +
1125A TYR* 2.8 63.9 + - + +
1126A GLN* 3.7 27.1 - - - +
1127A LEU 3.3 0.4 - - - -
1128A MET* 1.4 74.9 - - - +
1130A LYS* 1.4 56.6 + - - +
1132A TRP* 3.0 35.3 + - + +
1133A GLU* 3.8 5.6 + - - +
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Residues in contact with LYS1130 (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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1126A GLN* 3.2 20.6 + - - +
1127A LEU* 3.3 24.4 + - + +
1129A ARG* 1.4 74.0 - - + +
1131A CYS* 1.4 60.5 + - - +
1132A TRP 3.2 0.4 + - - -
1133A GLU* 4.1 10.5 + - + +
1138A ASN 5.8 0.7 - - - +
1139A ARG* 3.4 8.7 - - - +
1140A THR* 3.1 43.8 + - + +
1144A ASN* 4.7 9.0 - - - +
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Residues in contact with CYS1131 (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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1064A VAL* 3.4 33.4 - - - +
1065A TRP* 3.3 14.6 + - - +
1067A PHE* 4.0 4.5 - - - -
1068A GLY* 3.8 20.2 - - - -
1127A LEU 3.7 14.8 - - - -
1128A MET* 3.1 14.2 + - - +
1130A LYS* 1.4 76.5 - - - +
1132A TRP* 1.3 58.7 + - + +
1133A GLU 3.6 1.1 - - - -
1139A ARG* 3.2 21.4 - - - -
1140A THR* 3.9 0.7 - - - -
1145A LEU* 3.9 29.8 - - - -
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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