Contacts of the helix formed by residues 4118 - 4123 (chain F) in PDB entry 1Y1S
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 GLY4118 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1117A ASP 4.5 2.2 - - - -
1118A GLY* 3.8 13.5 - - - -
1160A ASP* 3.4 15.7 - - - -
1179A ARG* 5.2 0.3 + - - -
4117F ASP* 1.3 75.9 - - - +
4119F ALA* 1.3 66.7 + - - +
4120F SER 3.2 2.5 - - - -
4121F LEU* 3.0 28.4 + - - +
4122F HIS* 3.4 9.5 - - - -
4160F ASP* 3.2 9.3 + - - -
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Residues in contact with ALA4119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160A ASP* 3.4 19.7 + - + +
1161A THR* 4.1 17.3 - - + -
4071F GLY* 4.0 15.9 - - - +
4072F PRO* 4.3 1.1 - - + -
4117F ASP* 3.9 0.8 + - + +
4118F GLY* 1.3 74.7 - - - +
4120F SER* 1.3 56.5 + - - +
4122F HIS* 2.6 32.2 + - - +
4123F PHE* 3.3 9.1 - - - -
4160F ASP* 5.2 0.4 + - - +
4201F THR* 3.4 31.2 - - + +
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Residues in contact with SER4120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4115F ARG* 2.9 34.5 + - - -
4117F ASP* 2.7 36.9 + - - -
4119F ALA* 1.3 76.3 - - - +
4121F LEU* 1.3 67.4 + - - +
4122F HIS 3.0 1.6 + - - -
4123F PHE* 3.0 15.4 + - - -
4124F ALA 3.0 10.4 + - - -
4200F ALA 3.8 4.0 - - - -
4201F THR* 4.0 3.1 + - - +
4204F THR* 3.6 27.0 - - - +
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Residues in contact with LEU4121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177A VAL* 3.8 12.3 - - - +
1179A ARG* 4.1 31.5 + - - +
1180A PHE* 4.0 4.9 - - - -
4115F ARG* 3.4 14.1 - - - +
4117F ASP 3.5 21.3 - - - +
4118F GLY* 3.0 21.1 + - - +
4120F SER* 1.3 81.9 + - - +
4122F HIS* 1.3 59.4 + - - +
4123F PHE 3.2 1.6 + - - -
4124F ALA 3.4 11.7 - - - +
4125F PRO* 4.3 1.9 - - + +
4126F MET* 3.8 46.4 - - + +
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Residues in contact with HIS4122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116A LEU 3.0 26.7 + - - -
1159A SER* 3.1 24.0 - - - -
1160A ASP* 3.4 8.4 - - + +
1161A THR* 2.8 34.4 + - + +
1164A PRO* 3.1 30.1 - - + +
1165A GLY* 3.2 5.9 - - - -
1177A VAL* 3.7 10.0 + - - +
1179A ARG* 4.2 5.8 + - - -
1180A PHE* 3.2 36.3 - + + -
4118F GLY 3.4 17.9 + - - -
4119F ALA* 2.6 19.4 + - - +
4121F LEU* 1.3 73.7 - - - +
4123F PHE* 1.3 58.8 + - + +
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Residues in contact with PHE4123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161A THR* 4.0 13.5 - - + -
1164A PRO* 3.9 26.2 - - + -
1175A ARG* 3.0 33.0 + - - +
1177A VAL* 3.8 9.5 - - - +
6190B MET* 3.8 1.7 - - - +
4075F SER* 4.0 17.3 - - - -
4079F GLU* 5.3 4.3 - - + -
4119F ALA 3.3 22.2 - - - -
4120F SER* 3.0 7.7 + - - +
4122F HIS* 1.3 79.7 - - + +
4124F ALA* 1.3 65.6 + - - +
4201F THR* 4.5 2.2 - - + -
4204F THR* 4.5 0.9 - - + -
4205F MET* 3.6 42.6 - - + +
4208F SER* 3.8 14.5 + - - +
4209F GLN* 3.8 35.9 - - - -
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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