Contacts of the helix formed by residues 1120 - 1129 (chain A) in PDB entry 5IYB
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 GLY1120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102A MET 5.9 0.9 - - - -
1103A THR* 4.8 9.9 - - - -
1119A LEU* 1.3 82.3 - - - +
1121A VAL* 1.3 61.5 + - - -
1123A ARG* 3.1 7.9 + - - +
1124A LEU* 2.8 28.0 + - - +
1385A VAL* 4.5 17.5 - - - +
1389A ASP* 6.2 3.1 - - - -
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Residues in contact with VAL1121 (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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853A LYS* 5.8 5.6 - - + -
856A GLU* 4.6 28.0 - - + +
857A THR* 4.4 11.0 - - + -
860A ILE* 5.5 7.0 - - + -
1099A ALA* 3.2 35.0 - - + +
1102A MET 5.2 3.1 - - - +
1103A THR 4.4 12.7 + - - +
1104A LEU* 5.5 8.1 - - + -
1120A GLY* 1.3 68.4 - - - -
1122A PRO* 1.3 72.5 - - + +
1124A LEU* 3.5 12.4 - - + +
1125A LYS* 2.9 29.7 + - + +
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Residues in contact with PRO1122 (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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1104A LEU* 3.1 35.2 - - + +
1105A ASN* 4.9 8.5 - - + +
1118A THR* 3.6 20.8 - - + +
1119A LEU 3.8 4.5 - - - +
1120A GLY 3.8 2.5 - - - -
1121A VAL* 1.3 94.7 - - + +
1123A ARG* 1.3 55.9 + - - +
1125A LYS* 3.8 10.9 + - + +
1126A GLU* 3.1 25.5 + - - +
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Residues in contact with ARG1123 (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 VAL* 5.6 3.1 - - - +
1118A THR* 3.1 39.2 - - - +
1119A LEU 4.4 0.2 + - - -
1120A GLY 3.1 15.2 + - - +
1122A PRO* 1.3 77.5 - - - +
1124A LEU* 1.3 59.5 + - - +
1125A LYS 3.3 0.2 - - - -
1126A GLU* 2.4 39.0 + - - +
1127A LEU* 2.8 47.2 + - + +
1134A PRO* 5.1 4.9 - - - +
1136A THR 5.0 2.0 + - - -
1360A ASN* 2.6 44.1 + - - +
1381A GLU* 2.1 36.2 + - - +
1385A VAL* 3.4 22.8 - - + +
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Residues in contact with LEU1124 (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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860A ILE* 4.3 24.0 - - + -
864A LEU* 5.9 6.3 - - + -
1095A LEU* 5.2 15.5 - - + +
1099A ALA* 3.7 30.5 - - + -
1120A GLY 2.8 15.9 + - - +
1121A VAL* 3.2 15.0 + - + +
1123A ARG* 1.3 69.7 - - - +
1125A LYS* 1.3 60.8 + - - +
1127A LEU* 4.6 2.7 - - - -
1128A ILE* 2.9 45.2 + - + +
1382A LEU* 3.6 29.4 - - + -
1385A VAL* 5.1 9.6 - - + +
1386A ILE* 6.5 1.8 - - + -
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Residues in contact with LYS1125 (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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856A GLU* 3.1 35.2 + - - +
859A TYR* 6.3 0.7 - - + -
860A ILE* 4.3 20.4 - - + +
863A ARG* 4.8 10.8 - - - +
1121A VAL* 2.9 16.7 + - + +
1122A PRO* 4.0 9.2 - - + +
1124A LEU* 1.3 76.0 - - - +
1126A GLU* 1.3 63.4 + - - +
1128A ILE* 3.8 6.1 - - + +
1129A ASN* 3.1 34.6 + - + +
45X G 4.0 21.2 + - - -
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Residues in contact with GLU1126 (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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1118A THR* 4.0 10.9 + - - -
1122A PRO 3.1 16.2 + - - +
1123A ARG* 2.4 43.3 + - - +
1125A LYS* 1.3 81.3 - - - +
1127A LEU* 1.3 61.2 + - - +
1129A ASN* 3.9 1.9 + - - +
1131A SER* 3.4 32.9 + - - +
1134A PRO* 3.9 15.9 - - + -
1135A LYS* 2.5 48.7 + - + +
1136A THR 4.1 1.6 + - - -
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Residues in contact with LEU1127 (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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1123A ARG* 2.8 42.3 + - + +
1124A LEU* 4.0 2.5 - - - +
1126A GLU* 1.3 75.6 - - - +
1128A ILE* 1.3 64.4 + - + +
1130A ILE* 3.2 23.4 + - - +
1362A ILE* 3.6 30.9 - - + +
1378A LEU* 3.6 16.8 - - + +
1381A GLU* 3.8 28.3 - - + +
1382A LEU* 3.4 40.4 - - + +
1385A VAL* 6.0 0.9 - - + -
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Residues in contact with ILE1128 (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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860A ILE* 4.3 15.3 - - + -
863A ARG* 4.8 2.5 - - - +
864A LEU* 4.7 7.4 - - + -
1124A LEU* 2.9 34.1 + - + +
1125A LYS* 3.8 9.2 - - + +
1127A LEU* 1.3 75.6 - - + +
1129A ASN* 1.3 64.3 + - + +
1130A ILE* 3.2 1.6 + - - -
1378A LEU* 6.2 1.1 - - + -
1382A LEU* 4.7 9.4 - - + -
1401A LEU* 3.6 32.1 - - + -
1405A MET* 3.8 21.2 - - - +
1413A ALA* 3.8 3.6 - - - -
1414A ILE* 3.5 53.7 + - + -
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Residues in contact with ASN1129 (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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863A ARG* 4.0 9.0 - - - +
1125A LYS* 3.1 25.1 + - + +
1126A GLU* 4.4 4.0 - - - +
1127A LEU 3.3 0.4 - - - -
1128A ILE* 1.3 76.7 - - + +
1130A ILE* 1.3 67.1 + - - +
1131A SER* 4.4 5.1 - - - +
1413A ALA* 3.1 15.2 - - - +
1415A THR* 2.5 33.6 + - - +
1417A HIS* 4.0 13.6 + - - -
45X G 3.9 34.8 + - - -
46X C 4.6 7.5 - - - +
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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