Contacts of the helix formed by residues 1149 - 1159 (chain A) in PDB entry 4YOC
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 GLY1149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1143A ASP* 5.1 0.7 - - - -
1146A SER 3.4 9.2 + - - -
1147A GLY 3.1 3.2 - - - -
1148A CYS* 1.3 79.4 - - - +
1150A GLY* 1.3 61.5 + - - +
1151A LEU 3.4 2.5 - - - -
1152A SER* 4.0 4.5 - - - -
1153A GLU* 3.0 22.9 + - - +
1177A PHE* 3.5 24.5 - - - -
1181A ASN* 5.2 1.2 + - - -
1563A TYR* 2.8 16.6 + - - -
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Residues in contact with GLY1150 (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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1146A SER 4.6 2.0 + - - -
1148A CYS* 3.9 1.4 - - - -
1149A GLY* 1.3 74.8 - - - +
1151A LEU* 1.3 59.1 + - - +
1153A GLU* 3.1 4.7 + - - +
1154A GLY 2.9 25.3 + - - -
1559A PHE* 3.9 26.0 - - - -
1579A ALA* 4.6 6.0 - - - +
1580A VAL 3.6 20.2 - - - -
1582A PRO* 3.8 9.8 - - - +
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Residues in contact with LEU1151 (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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1143A ASP* 4.2 11.0 - - - +
1146A SER 5.5 3.3 + - - +
1149A GLY* 3.4 0.8 - - - -
1150A GLY* 1.3 76.5 - - - +
1152A SER* 1.3 57.5 + - - +
1154A GLY 3.3 1.6 + - - -
1155A PHE* 2.9 52.2 + - + +
1221A CYS* 3.8 28.7 - - + -
1222A GLY* 4.2 14.1 - - - +
1264A LEU* 4.8 13.0 - - + -
1266A GLU* 4.6 15.3 - - + -
1580A VAL* 4.0 28.9 + - + +
1585A ALA* 3.6 27.5 - - + +
1588A ILE* 5.7 2.2 - - + -
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Residues in contact with SER1152 (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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1143A ASP* 2.4 34.5 + - - +
1149A GLY 3.7 3.7 + - - -
1150A GLY 3.4 0.2 - - - -
1151A LEU* 1.3 78.2 - - - +
1153A GLU* 1.3 54.2 + - - +
1155A PHE* 3.8 8.0 - - - +
1156A HIS* 2.7 46.9 + - - -
1163A THR* 3.2 24.2 + - - -
1177A PHE* 3.6 22.9 - - - -
1181A ASN* 5.1 1.3 - - - -
1221A CYS* 4.7 1.6 - - - -
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Residues in contact with GLU1153 (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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1149A GLY 3.0 21.0 + - - +
1150A GLY* 3.3 8.1 - - - +
1151A LEU 3.1 0.2 - - - -
1152A SER* 1.3 73.6 - - - +
1154A GLY* 1.3 60.9 + - - +
1156A HIS* 3.0 14.9 + - - +
1157A GLN* 2.9 61.8 + - - +
1180A ASN* 5.5 2.6 - - - +
1181A ASN* 5.6 1.2 - - - +
1560A PRO* 4.1 9.8 - - + +
1563A TYR* 3.4 31.7 - - + -
1582A PRO* 4.1 12.1 - - + -
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Residues in contact with GLY1154 (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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1150A GLY 2.9 13.3 + - - -
1151A LEU 3.8 2.2 - - - -
1153A GLU* 1.3 76.8 - - - +
1155A PHE* 1.3 57.1 + - - +
1157A GLN* 3.1 9.8 + - - +
1158A ALA* 2.9 22.5 + - - +
1582A PRO* 3.3 29.1 - - - +
1585A ALA* 3.9 3.4 - - - -
1586A LYS* 3.4 16.2 - - - -
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Residues in contact with PHE1155 (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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1141A THR* 5.1 2.2 - - + -
1151A LEU* 2.9 25.9 + - + +
1152A SER* 3.8 5.6 - - - +
1153A GLU 3.2 0.2 - - - -
1154A GLY* 1.3 73.1 - - - +
1156A HIS* 1.3 64.2 + - - +
1158A ALA* 3.1 13.9 + - - +
1159A GLY 3.2 8.7 + - - -
1160A ILE* 3.6 11.5 + - + +
1161A SER* 3.2 22.5 + - - +
1219A MET* 4.0 26.7 - - + -
1221A CYS* 4.0 30.7 - - + -
1264A LEU* 3.5 28.9 - - + -
1585A ALA* 3.1 31.6 - - + -
1588A ILE* 4.4 1.6 - - + -
1589A GLY* 3.8 19.7 - - - -
1592A ILE* 4.4 9.2 - - + -
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Residues in contact with HIS1156 (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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1138A LYS* 3.9 7.7 + - - +
1152A SER* 2.7 31.4 + - - +
1153A GLU* 3.0 15.7 + - - +
1155A PHE* 1.3 75.5 - - - +
1157A GLN* 1.3 61.1 + - + +
1159A GLY* 3.2 13.2 + - - +
1161A SER* 3.0 36.3 - - - -
1162A ASP* 3.8 6.9 + - - -
1163A THR* 3.1 38.6 + - - -
1181A ASN* 3.2 27.3 + - - -
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Residues in contact with GLN1157 (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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1153A GLU* 2.9 48.5 + - - +
1154A GLY* 3.1 10.1 + - - +
1156A HIS* 1.3 76.4 - - + +
1158A ALA* 1.3 63.7 + - - +
1159A GLY* 3.1 1.7 + - - -
1560A PRO* 4.0 16.4 - - - +
1582A PRO* 4.3 15.6 - - - +
1583A PRO* 5.3 1.0 - - - +
1586A LYS* 3.8 35.7 + - + +
1590A LEU* 5.4 0.3 - - - +
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Residues in contact with ALA1158 (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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1154A GLY 2.9 11.7 + - - +
1155A PHE 3.1 10.3 + - - +
1157A GLN* 1.3 77.7 - - - +
1159A GLY* 1.3 60.9 + - - +
1160A ILE* 4.2 4.3 - - + -
1586A LYS* 3.8 9.8 - - - +
1589A GLY* 3.6 39.5 - - - +
1590A LEU* 3.7 14.4 - - + +
1593A LYS* 3.5 27.2 + - - +
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Residues in contact with GLY1159 (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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1136A LEU* 4.9 9.4 - - - +
1138A LYS* 3.4 33.8 + - - +
1155A PHE 3.2 1.2 + - - -
1156A HIS 3.2 6.5 + - - -
1157A GLN 3.1 5.1 - - - -
1158A ALA* 1.3 79.6 - - - +
1160A ILE* 1.3 61.0 + - - +
1593A LYS* 4.6 12.1 + - - -
1596A MET* 5.8 0.2 - - - +
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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