Contacts of the helix formed by residues 1116 - 1122 (chain B) in PDB entry 4E70
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 ARG1116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1033B LEU* 3.0 56.0 + - + +
1034B GLU* 5.5 0.2 - - - +
1036B ASP* 3.4 12.1 + - - +
1039B ASP* 4.2 8.1 + - - -
1107B LEU* 3.5 25.5 + - - +
1109B LYS* 3.4 43.3 - - - +
1114B ASN* 2.9 20.9 + - - +
1115B ALA* 1.3 76.3 - - - +
1117B SER* 1.3 67.3 + - - +
1119B THR* 3.2 4.3 + - - -
1120B PHE* 3.0 51.0 + - + -
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Residues in contact with SER1117 (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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1114B ASN* 4.4 2.8 + - - -
1115B ALA 3.5 0.2 - - - -
1116B ARG* 1.3 79.1 - - - +
1118B LEU* 1.3 57.9 + - - +
1120B PHE* 3.3 3.6 + - - +
1121B CYS* 2.9 30.5 + - - +
1174B LEU* 3.5 35.2 - - - +
1177B GLU* 2.7 40.2 + - - +
1178B GLY* 3.9 2.9 - - - -
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Residues in contact with LEU1118 (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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17A TRP* 3.8 26.9 - - + +
20A PHE* 3.9 11.2 - - + -
1115B ALA* 3.4 14.8 + - + +
1116B ARG 3.3 0.4 - - - -
1117B SER* 1.3 78.5 - - - +
1119B THR* 1.3 55.6 + - - +
1121B CYS* 3.6 6.1 - - + +
1122B SER* 2.7 36.8 + - - -
1175B PHE* 5.0 2.5 - - + -
1178B GLY* 3.9 26.7 - - - +
1179B MET* 3.7 28.0 - - + -
1182B ASP* 5.7 2.5 - - + -
1268B TRP* 5.1 3.6 - - + -
1402B N7I 3.7 40.4 - - + +
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Residues in contact with THR1119 (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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16A VAL* 4.6 1.6 - - - +
20A PHE* 3.1 41.1 - - + -
1029B LEU* 4.3 14.5 - - + +
1030B GLN* 4.7 10.5 - - + +
1033B LEU* 3.5 24.0 - - + +
1107B LEU* 5.7 1.0 - - - +
1115B ALA* 2.8 21.2 + - - +
1116B ARG 3.2 8.5 + - - -
1118B LEU* 1.3 77.2 - - - +
1120B PHE* 1.3 64.3 + - + +
1122B SER* 3.2 1.7 + - - -
1123B VAL* 3.1 30.6 + - + +
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Residues in contact with PHE1120 (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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1030B GLN* 3.6 32.0 - - + +
1033B LEU* 3.5 36.6 - - + -
1034B GLU* 4.0 14.1 - - + -
1116B ARG* 3.0 55.5 + - + +
1117B SER* 3.8 7.2 - - - +
1119B THR* 1.3 75.1 - - - +
1121B CYS* 1.3 63.2 + - - +
1123B VAL* 3.9 5.9 - - - +
1124B HIS* 3.3 24.1 + - - +
1174B LEU* 3.8 25.7 - - + +
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Residues in contact with CYS1121 (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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1117B SER 2.9 17.3 + - - +
1118B LEU* 3.6 8.1 - - + +
1120B PHE* 1.3 78.0 - - - +
1122B SER* 1.3 61.4 + - - +
1124B HIS* 3.2 20.8 + - - +
1127B LEU* 3.5 12.1 - - - +
1171B PHE* 3.7 24.7 - - - -
1174B LEU* 3.9 19.2 - - + +
1175B PHE* 3.9 26.0 - - - -
1402B N7I 3.7 23.6 - - - -
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Residues in contact with SER1122 (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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20A PHE* 3.2 26.3 - - - -
21A LEU* 3.9 8.5 - - - -
23A TYR* 2.7 29.5 + - - -
1118B LEU 2.7 21.5 + - - -
1119B THR 3.2 0.6 + - - -
1121B CYS* 1.3 78.0 - - - +
1123B VAL* 1.3 60.0 + - - +
1124B HIS 3.3 0.8 + - - -
1127B LEU* 3.9 14.2 - - - +
1128B VAL* 4.2 0.2 - - - +
1325B LEU* 5.7 0.2 - - - -
1402B N7I 2.8 32.7 + - - -
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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