Contacts of the helix formed by residues 1107 - 1122 (chain A) in PDB entry 4YKN
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 ASN1107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1083A PHE* 5.1 0.4 - - - -
1106A GLY* 1.3 71.1 - - - -
1108A ARG* 1.3 66.7 + - - +
1109A GLU* 3.4 17.3 + - - +
1110A GLU* 2.9 42.6 + - + +
1111A LYS* 3.2 27.0 + - - +
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Residues in contact with ARG1108 (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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1069A ILE* 6.2 0.6 - - - +
1083A PHE* 2.6 57.6 + - + +
1084A ASP* 4.8 5.1 + - - +
1085A GLU* 5.5 2.2 - - - +
1106A GLY 3.5 4.0 + - - +
1107A ASN* 1.3 73.2 - - - +
1109A GLU* 1.3 82.5 + - - +
1110A GLU 3.4 0.2 + - - -
1111A LYS* 3.4 3.6 + - - +
1112A ILE* 3.1 47.8 + - + +
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Residues in contact with GLU1109 (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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1107A ASN* 3.4 15.2 + - - +
1108A ARG* 1.3 104.4 + - - +
1110A GLU* 1.3 56.9 + - - +
1112A ILE* 3.8 9.2 - - + +
1113A LEU* 3.1 27.4 + - - +
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Residues in contact with GLU1110 (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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1107A ASN* 2.9 29.0 + - + +
1108A ARG 3.3 0.2 - - - -
1109A GLU* 1.3 75.2 - - - +
1111A LYS* 1.3 60.7 + - + +
1113A LEU* 3.2 8.3 + - + +
1114A ASN* 2.8 55.8 + - - +
1303A THR* 6.0 1.4 - - - +
1304A MET 4.8 1.4 - - - +
1305A PRO* 3.9 14.7 - - + +
1306A SER* 3.1 48.6 + - - -
1307A TYR* 5.2 2.9 - - - -
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Residues in contact with LYS1111 (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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1081A GLU* 3.4 27.5 - - + +
1083A PHE* 3.5 33.7 - - + -
1105A VAL 4.3 9.2 - - - -
1106A GLY* 5.1 4.3 - - - -
1107A ASN 3.2 19.8 + - - +
1108A ARG 3.4 1.1 + - - +
1110A GLU* 1.3 78.7 - - + +
1112A ILE* 1.3 62.3 + - - +
1114A ASN* 3.3 14.0 + - + +
1115A ARG* 3.1 22.2 + - - +
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Residues in contact with ILE1112 (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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1083A PHE* 3.5 19.5 - - + -
1084A ASP* 4.0 26.0 - - + +
1108A ARG* 3.1 58.6 + - + +
1109A GLU* 3.8 9.2 - - + +
1111A LYS* 1.3 75.3 - - - +
1113A LEU* 1.3 62.6 + - - +
1115A ARG* 3.3 7.6 + - - +
1116A GLU* 3.3 39.5 + - + +
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Residues in contact with LEU1113 (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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1109A GLU 3.1 18.7 + - - +
1110A GLU* 3.7 8.3 - - + +
1112A ILE* 1.3 74.2 - - - +
1114A ASN* 1.3 63.2 + - - +
1116A GLU* 3.0 23.0 + - + +
1117A ILE* 2.8 52.6 + - + +
1303A THR 6.0 1.3 - - - +
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Residues in contact with ASN1114 (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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1110A GLU* 2.8 48.9 + - - +
1111A LYS* 3.3 17.8 + - + +
1113A LEU* 1.3 74.2 - - - +
1115A ARG* 1.3 57.2 + - - +
1117A ILE* 3.8 15.6 - - - +
1118A GLY* 2.9 26.9 + - - -
1125A VAL* 4.1 34.0 + - + +
1129A ASP* 5.9 0.4 + - - -
1305A PRO* 6.0 1.0 - - - +
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Residues in contact with ARG1115 (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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1078A GLU* 6.0 0.9 - - - +
1080A GLU* 3.1 30.1 - - + +
1081A GLU 5.9 1.1 - - - +
1084A ASP* 5.1 4.6 + - - -
1087A ARG* 3.3 51.1 - - - +
1111A LYS 3.1 12.3 + - - +
1112A ILE* 3.5 10.5 + - - +
1113A LEU 3.2 0.2 - - - -
1114A ASN* 1.3 77.4 - - - +
1116A GLU* 1.3 79.5 + - - +
1118A GLY* 3.4 1.5 + - - -
1119A PHE* 3.1 50.0 + - - +
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Residues in contact with GLU1116 (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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1084A ASP* 5.2 2.9 - - - +
1112A ILE* 3.3 31.1 + - + +
1113A LEU* 3.0 22.8 + - + +
1115A ARG* 1.3 98.2 + - - +
1117A ILE* 1.3 62.4 + - - +
1119A PHE* 3.5 5.9 + - - +
1120A ALA* 3.3 20.3 + - - +
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Residues in contact with ILE1117 (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 LEU* 2.8 50.8 + - + +
1114A ASN* 3.8 13.7 - - - +
1116A GLU* 1.3 73.7 - - - +
1118A GLY* 1.3 61.2 + - - +
1120A ALA* 3.1 7.2 + - - +
1121A ILE* 2.9 49.9 + - + +
1125A VAL* 3.9 13.0 - - + -
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Residues in contact with GLY1118 (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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1114A ASN 2.9 16.5 + - - -
1115A ARG* 3.8 1.8 - - - -
1117A ILE* 1.3 78.1 - - - +
1119A PHE* 1.3 57.7 + - - +
1121A ILE* 4.4 2.2 - - - -
1122A GLY* 3.0 23.7 + - - -
1123A MET 3.1 28.8 + - - +
1124A PRO* 4.7 2.5 - - - -
1125A VAL* 4.3 9.1 - - - +
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Residues in contact with PHE1119 (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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1091A ASP 6.1 0.4 - - - -
1093A ARG* 4.6 34.5 - - - +
1115A ARG* 3.1 39.2 + - - +
1116A GLU* 3.7 6.5 - - - +
1117A ILE 3.1 0.2 - - - -
1118A GLY* 1.3 77.5 - - - +
1120A ALA* 1.3 65.4 + - - +
1122A GLY* 3.4 10.0 + - - -
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Residues in contact with ALA1120 (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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1116A GLU 3.3 9.6 + - - +
1117A ILE* 3.1 9.4 + - + +
1119A PHE* 1.3 84.5 - - + +
1121A ILE* 1.3 65.0 + - + +
1122A GLY* 3.4 0.7 + - - -
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Residues in contact with ILE1121 (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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1117A ILE* 2.9 39.1 + - + +
1118A GLY 4.0 2.5 - - - +
1120A ALA* 1.3 79.7 - - + +
1122A GLY* 1.3 57.8 + - - +
1123A MET* 3.5 36.7 - - + +
1125A VAL* 4.7 7.0 - - + -
1128A PHE* 4.7 17.3 - - + -
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Residues in contact with GLY1122 (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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1076A GLU* 4.4 13.2 - - - -
1118A GLY 3.0 9.6 + - - -
1119A PHE* 3.4 6.2 + - - -
1120A ALA 3.2 4.0 + - - -
1121A ILE* 1.3 76.9 - - - +
1123A MET* 1.3 58.9 + - - +
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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