Contacts of the helix formed by residues 1049 - 1056 (chain B) in PDB entry 4E4N
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 ALA1049 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047B TRP 4.0 0.2 + - - -
1048B TYR* 1.3 75.5 - - - +
1050B PRO* 1.3 76.3 - - + +
1051B GLU* 3.3 28.0 - - - +
1052B CYS* 3.1 22.6 + - - +
1053B LEU* 3.1 11.7 + - - +
1062B SER* 4.3 4.1 + - - -
1065B TRP* 3.6 26.8 - - + +
1139B ARG* 3.7 7.6 - - - +
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Residues in contact with PRO1050 (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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1048B TYR 3.9 0.6 - - - +
1049B ALA* 1.3 88.1 - - + +
1051B GLU* 1.3 53.5 + - - +
1053B LEU* 3.1 10.5 + - + +
1054B MET* 2.7 49.1 + - + +
1065B TRP* 3.5 30.5 - - + -
1105B VAL* 5.4 2.5 - - + -
1108B LEU* 4.3 8.5 - - + -
1134B PHE* 3.6 53.4 - - + +
1139B ARG* 3.7 4.9 - - - +
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Residues in contact with GLU1051 (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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1049B ALA* 3.3 10.3 - - - +
1050B PRO* 1.3 75.1 - - - +
1052B CYS* 1.3 57.4 + - - +
1054B MET* 4.1 8.0 - - + +
1055B GLN* 3.0 35.5 + - - +
1056B SER 3.2 6.1 + - - -
1057B LYS* 3.3 23.4 + - + +
1059B TYR* 3.8 20.9 - - + -
1062B SER* 2.7 21.4 + - - +
1134B PHE 4.1 1.6 - - - +
1136B PRO* 3.8 20.6 - - + +
1139B ARG* 2.8 40.2 + - - -
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Residues in contact with CYS1052 (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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1099A MET* 5.0 2.8 - - - +
1048B TYR* 3.9 15.8 - - + -
1049B ALA* 3.1 23.6 + - - +
1051B GLU* 1.3 77.2 - - - +
1053B LEU* 1.3 59.9 + - - +
1056B SER* 3.0 26.0 + - - +
1057B LYS 3.6 13.0 - - - +
1058B PHE* 3.6 31.1 - - + -
1062B SER* 3.5 35.7 - - - -
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Residues in contact with LEU1053 (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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1099A MET* 3.4 18.4 - - + +
1102A THR* 3.3 16.5 + - - +
1045B VAL* 3.7 39.0 - - + +
1048B TYR* 3.8 29.2 - - + +
1049B ALA 3.1 13.4 + - - +
1050B PRO* 3.7 4.5 - - + +
1052B CYS* 1.3 78.4 - - - +
1054B MET* 1.3 62.2 + - - +
1055B GLN 3.8 0.2 + - - -
1056B SER 4.7 0.5 + - - -
1101B VAL* 4.1 13.2 - - + -
1104B LEU* 3.9 20.6 - - + -
1105B VAL* 3.8 26.5 - - + -
1108B LEU* 4.1 13.7 - - + -
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Residues in contact with MET1054 (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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1102A THR* 3.6 12.8 - - + +
1106A ASN* 2.6 37.0 + - - +
1109A LYS* 6.2 1.1 - - - -
1050B PRO* 2.7 44.3 + - + +
1051B GLU* 4.1 5.4 - - + +
1053B LEU* 1.3 73.2 - - - +
1055B GLN* 1.3 65.1 + - + +
1056B SER 3.9 0.2 - - - -
1105B VAL* 3.9 23.3 - - + -
1109B LYS* 4.0 28.3 - - - -
1134B PHE* 3.8 17.5 - - + -
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Residues in contact with GLN1055 (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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1106A ASN* 4.4 9.0 - - - +
1036B THR* 4.2 5.9 - - - +
1051B GLU* 3.0 22.2 + - - +
1054B MET* 1.3 92.1 - - + +
1056B SER* 1.3 79.3 + - - +
1057B LYS* 3.1 41.1 + - + +
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Residues in contact with SER1056 (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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1103A ARG* 3.6 23.7 + - - +
1106A ASN* 5.9 0.2 + - - -
1036B THR* 3.3 7.4 - - - +
1037B VAL* 3.0 43.9 + - - -
1040B ASP* 4.9 7.9 - - - -
1051B GLU 3.2 0.4 + - - -
1052B CYS 3.0 22.1 + - - -
1053B LEU 4.6 0.6 + - - -
1054B MET 3.9 0.4 - - - -
1055B GLN* 1.3 82.6 + - - +
1057B LYS* 1.3 57.4 + - - +
1058B PHE* 3.6 14.5 - - - -
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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