Contacts of the helix formed by residues 1099 - 1107 (chain B) in PDB entry 5IY8
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 ALA1099 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514A GLU* 2.9 39.3 - - + +
515A ILE* 5.9 2.7 - - + -
518A LEU* 4.1 8.5 - - + -
519A ALA* 5.9 3.4 - - + -
1094B GLN* 3.3 29.4 + - - +
1097B HIS* 4.5 6.3 - - + -
1098B GLY* 1.3 78.4 - - - +
1100B ALA* 1.3 59.6 + - - +
1102B PHE* 3.6 2.2 - - + +
1103B LEU* 3.0 19.6 + - - +
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Residues in contact with ALA1100 (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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1458A ILE* 5.4 1.4 - - - +
1463A LEU* 4.0 7.9 - - + +
1464A ALA* 4.0 22.3 + - + +
1466A ALA* 3.2 28.3 - - + +
1468A THR* 3.0 12.6 + - - +
1469A GLY* 3.8 6.7 - - - +
1098B GLY* 3.5 1.2 - - - -
1099B ALA* 1.3 74.6 - - - +
1101B GLN* 1.3 56.3 + - - +
1103B LEU* 3.2 11.1 + - - +
1104B ARG* 2.9 29.6 + - - +
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Residues in contact with GLN1101 (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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510A GLU* 3.1 52.4 + - - +
511A THR* 4.1 10.1 - - + +
514A GLU* 3.1 18.9 + - - +
1463A LEU* 3.8 23.3 - - + -
1468A THR* 4.0 5.5 - - - +
1099B ALA 3.1 0.2 + - - -
1100B ALA* 1.3 73.1 - - - +
1102B PHE* 1.3 62.2 + - - +
1104B ARG* 3.5 11.6 + - - +
1105B GLU* 3.1 26.7 + - - +
63F ALA 5.3 1.9 - - - +
64F ARG* 2.8 48.1 - - - +
68F THR* 5.8 0.4 + - - -
61G PRO* 5.4 2.4 - - + +
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Residues in contact with PHE1102 (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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457A ILE* 4.2 31.9 - - + -
469A MET* 5.7 0.2 - - + -
504A HIS* 4.6 5.8 - - + -
506A PRO* 4.4 8.5 - - + -
511A THR* 3.8 21.6 - - + +
514A GLU* 2.9 19.7 + - - +
515A ILE* 4.1 26.9 - - + -
1086B PHE* 5.0 2.9 - + - -
1094B GLN* 3.0 37.5 - - + +
1099B ALA* 3.6 3.4 - - + +
1101B GLN* 1.3 76.0 - - - +
1103B LEU* 1.3 58.3 + - - +
1105B GLU* 3.6 9.8 - - - +
1106B ARG* 3.1 68.5 + - + +
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Residues in contact with LEU1103 (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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1454A VAL* 5.7 0.9 - - + -
1458A ILE* 3.8 28.9 - - + +
1464A ALA* 5.6 1.6 - - + -
1086B PHE* 4.3 4.5 - - + -
1091B ARG* 4.0 24.7 - - + +
1094B GLN* 4.0 23.8 - - + +
1095B ILE* 3.8 30.3 - - + +
1099B ALA 3.0 14.0 + - - +
1100B ALA* 3.2 15.0 + - - +
1102B PHE* 1.3 75.2 - - - +
1104B ARG* 1.3 65.0 + - - +
1106B ARG* 4.3 1.3 - - + +
1107B LEU* 3.3 34.9 + - + +
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Residues in contact with ARG1104 (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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510A GLU* 4.7 8.7 + - - -
1458A ILE* 4.8 10.7 - - + +
1461A GLY* 3.2 30.1 - - - +
1462A GLN* 4.8 2.7 - - - +
1463A LEU* 4.0 43.4 - - + +
1464A ALA 5.4 0.2 - - - +
1100B ALA 2.9 18.2 + - - +
1101B GLN* 3.5 10.6 + - - +
1103B LEU* 1.3 74.1 - - - +
1105B GLU* 1.3 64.0 + - - +
1107B LEU* 3.4 2.8 - - - -
1108B PHE* 2.9 55.0 + - + +
1109B GLU* 5.3 8.1 + - - +
61G PRO* 4.0 35.5 + - - +
62G GLY* 5.0 1.8 - - - -
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Residues in contact with GLU1105 (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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506A PRO* 4.0 2.6 - - - +
507A GLN* 3.6 27.5 + - + +
508A SER* 4.5 3.3 + - - -
511A THR* 3.0 32.6 + - + +
1101B GLN 3.1 18.7 + - - +
1102B PHE* 3.6 9.3 - - - +
1103B LEU 3.2 0.2 - - - -
1104B ARG* 1.3 79.3 - - - +
1106B ARG* 1.3 96.9 + - - +
1109B GLU* 3.5 27.4 + - + +
1110B ALA* 3.1 34.8 + - + +
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Residues in contact with ARG1106 (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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357A LYS* 5.1 0.3 - - - +
359A VAL* 3.5 27.4 - - + +
360A ASP 3.5 24.4 + - - -
361A PHE* 3.8 4.8 + - - +
504A HIS* 3.3 32.2 + - - +
505A LEU 2.2 33.8 + - - +
507A GLN* 4.2 6.7 - - - +
1086B PHE* 4.0 28.3 - - + -
1102B PHE* 3.1 49.9 + - + +
1103B LEU* 4.3 1.3 - - - +
1105B GLU* 1.3 97.2 + - - +
1107B LEU* 1.3 69.7 + - + +
1108B PHE 3.4 4.4 + - - -
1110B ALA* 4.2 11.0 - - - +
1111B SER* 3.6 10.9 + - - -
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Residues in contact with LEU1107 (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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354A LEU 4.6 3.4 - - - +
355A MET* 3.2 33.0 - - - +
357A LYS* 3.8 32.9 - - + +
359A VAL* 5.6 0.2 - - + -
1458A ILE* 3.9 35.3 - - + +
1461A GLY* 5.5 0.5 - - - -
1086B PHE* 3.4 42.4 - - + +
1091B ARG* 4.3 10.3 - - + -
1103B LEU* 3.3 22.1 + - + +
1104B ARG* 3.4 3.7 - - - +
1106B ARG* 1.3 77.5 - - + +
1108B PHE* 1.3 63.1 + - - +
1152B PRO* 4.9 2.9 - - - +
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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