Contacts of the helix formed by residues 1061 - 1073 (chain B) in PDB entry 4Z4Q
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 LYS1061 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581A LYS* 6.0 2.7 - - - -
585A GLU* 3.3 25.8 + - - +
1070A MET* 4.2 21.3 - - + -
1071A GLY* 4.1 21.5 - - - +
1060B ARG* 1.3 73.5 - - - +
1062B SER* 1.3 66.9 + - - +
1063B ALA* 3.8 15.7 - - + +
1064B LYS* 2.9 19.2 + - + +
1065B SER* 3.3 8.5 + - - -
1116B MET 3.7 7.2 - - - +
1117B ARG* 3.4 23.8 + - - +
1118B TYR 3.3 22.6 + - - -
1119B THR 3.5 16.8 + - - +
1120B GLU* 4.3 6.8 + - - +
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Residues in contact with SER1062 (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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1060B ARG 3.1 4.5 + - - -
1061B LYS* 1.3 70.3 - - - +
1063B ALA* 1.3 59.2 + - - +
1065B SER* 2.9 11.2 + - - +
1066B VAL* 2.8 32.3 + - - +
1082B TYR* 3.6 21.9 - - - -
1085B MET* 4.7 5.5 - - - +
1101B MET* 4.5 2.9 - - - +
1116B MET 3.6 6.1 - - - -
1119B THR* 2.6 44.6 + - - -
1120B GLU 3.9 7.6 + - - -
1121B ALA* 4.1 8.1 - - - +
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Residues in contact with ALA1063 (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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1063A ALA 5.1 0.2 - - - +
1067A GLY* 3.9 11.5 - - - -
1070A MET* 3.8 31.2 - - + -
1078A ASP* 5.9 0.4 - - + -
1061B LYS* 3.3 2.7 - - + -
1062B SER* 1.3 75.7 - - - +
1064B LYS* 1.3 61.6 + - - +
1066B VAL* 3.8 0.5 - - - +
1067B GLY* 3.0 22.5 + - - -
1116B MET* 3.0 49.8 + - + +
1117B ARG* 4.6 0.4 - - + -
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Residues in contact with LYS1064 (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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1067A GLY* 3.5 26.3 + - - +
1068A ASN* 3.7 21.8 - - - +
1071A GLY* 4.4 13.0 - - - -
1072A ASN* 3.1 33.6 + - - +
1060B ARG* 3.8 41.0 - - + +
1061B LYS* 2.9 15.1 + - + +
1063B ALA* 1.3 77.7 - - - +
1065B SER* 1.3 62.2 + - - +
1067B GLY* 4.2 0.5 - - - -
1068B ASN* 3.2 38.8 + - - +
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Residues in contact with SER1065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047B SER* 4.7 0.9 + - - -
1048B MET* 4.3 18.7 - - - +
1051B ASP* 6.0 0.2 - - - -
1053B ASN* 3.2 26.3 + - - -
1060B ARG* 3.8 10.1 + - - +
1061B LYS 3.3 4.9 + - - -
1062B SER* 2.9 10.0 + - - -
1064B LYS* 1.3 76.7 - - - +
1066B VAL* 1.3 64.4 + - - +
1068B ASN* 3.2 8.5 + - - +
1069B ILE* 3.0 29.0 + - - +
1085B MET* 4.4 13.9 - - - -
1121B ALA* 5.4 1.6 - - - +
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Residues in contact with VAL1066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062B SER 2.8 17.5 + - - +
1063B ALA 3.8 0.7 - - - +
1065B SER* 1.3 76.9 - - - +
1067B GLY* 1.3 58.1 + - - +
1069B ILE* 3.3 10.8 + - - +
1070B MET* 2.9 32.0 + - + +
1078B ASP* 3.8 26.7 - - + +
1081B ILE* 4.2 11.0 - - + +
1082B TYR* 4.0 30.7 - - + +
1085B MET* 4.5 7.9 - - - -
1116B MET* 3.7 33.0 - - + -
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Residues in contact with GLY1067 (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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1061A LYS* 5.8 0.2 - - - +
1063A ALA* 3.9 24.0 - - - -
1064A LYS* 3.5 18.7 + - - +
1067A GLY* 5.6 0.7 - - - -
1063B ALA 3.0 15.7 + - - -
1064B LYS 4.2 0.7 - - - -
1066B VAL* 1.3 76.5 - - - +
1068B ASN* 1.3 65.3 + - - +
1070B MET* 3.3 5.8 + - - +
1071B GLY 2.9 19.4 + - - -
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Residues in contact with ASN1068 (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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1064A LYS* 3.7 25.9 + - - +
1068A ASN* 3.7 10.9 + - - +
1047B SER* 4.1 6.5 - - - +
1051B ASP* 3.2 27.6 + - - +
1060B ARG* 5.3 1.6 - - - +
1064B LYS* 3.2 38.9 + - - +
1065B SER* 3.2 7.4 + - - +
1067B GLY* 1.3 75.0 - - - +
1069B ILE* 1.3 58.9 + - - +
1071B GLY 3.2 0.3 + - - -
1072B ASN* 2.9 47.4 + - - +
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Residues in contact with ILE1069 (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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1040B VAL* 5.7 0.7 - - + +
1043B ARG* 4.1 11.4 - - + +
1044B ILE* 3.7 39.9 - - + +
1047B SER* 3.5 25.6 - - - -
1048B MET* 4.9 2.7 - - + -
1065B SER* 3.0 30.6 + - - +
1066B VAL* 3.5 5.8 - - - +
1068B ASN* 1.3 75.4 - - - +
1070B MET* 1.3 59.3 + - - +
1073B PHE* 2.9 32.0 + - + -
1074B HIS* 3.1 21.6 + - + +
1081B ILE* 3.6 32.1 - - + -
1085B MET* 5.5 2.7 - - - -
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Residues in contact with MET1070 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061A LYS* 4.4 20.1 - - + +
1063A ALA* 3.9 25.6 - - + -
1117A ARG* 4.0 23.6 - - - +
1066B VAL* 2.9 24.7 + - + +
1067B GLY* 3.3 5.1 + - - +
1069B ILE* 1.3 75.4 - - - +
1071B GLY* 1.3 58.8 + - - +
1073B PHE 4.6 0.2 - - - -
1074B HIS 3.4 17.6 - - - +
1075B PRO* 4.6 2.8 - - + +
1076B HIS 3.7 21.1 - - - +
1078B ASP* 3.1 44.9 - - + +
1081B ILE* 3.7 5.6 - - + -
1145B PHE* 4.0 10.7 - - - -
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Residues in contact with GLY1071 (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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1061A LYS* 4.4 18.2 - - - -
1064A LYS* 4.4 11.2 - - - -
1067B GLY 2.9 15.8 + - - -
1068B ASN 3.7 0.4 - - - -
1070B MET* 1.3 79.6 - - - +
1072B ASN* 1.3 67.0 + - - +
1145B PHE* 3.4 16.0 - - - -
1146B ASP* 3.7 13.0 - - - +
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Residues in contact with ASN1072 (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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1064A LYS* 3.0 30.8 + - - +
1047B SER* 5.0 1.0 + - - -
1050B LYS* 6.0 1.2 - - - +
1051B ASP* 5.6 1.4 + - - -
1068B ASN* 2.9 32.0 + - - +
1071B GLY* 1.3 82.9 - - - +
1073B PHE* 1.3 86.1 + - + +
1144B ASN* 2.8 30.9 + - - +
1145B PHE* 4.2 3.9 - - - -
1146B ASP* 5.2 1.2 - - - +
1149B GLU* 3.7 21.0 + - - +
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Residues in contact with PHE1073 (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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1043B ARG* 3.4 47.0 + - + +
1046B TYR* 3.7 22.2 - + - -
1047B SER* 3.9 36.8 - - - -
1050B LYS* 4.6 3.4 - - + -
1069B ILE* 2.9 13.2 + - - +
1071B GLY 3.7 0.8 - - - -
1072B ASN* 1.3 101.4 - - + +
1074B HIS* 1.3 57.3 + - + +
1075B PRO* 3.5 7.1 - - - +
1144B ASN* 4.6 5.0 - - + +
1145B PHE* 3.6 13.4 + - - -
1149B GLU* 3.5 31.9 - - + -
1150B LYS 3.9 20.2 - - - -
1151B GLU* 3.8 22.5 - - + +
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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