Contacts of the strand formed by residues 4107 - 4116 (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 VAL4107 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4105F GLY 4.3 1.8 - - - +
4106F ASP* 1.3 74.8 - - - +
4108F LEU* 1.3 66.5 - - - +
4109F VAL* 5.0 1.6 - - + -
4144F ALA* 5.2 0.4 - - + -
4149F ALA* 3.8 15.7 - - + -
4150F THR 3.0 9.0 + - - +
4151F THR* 3.3 15.4 - - + +
4152F HIS 3.2 22.7 + - - -
4216F VAL* 3.5 28.5 - - + -
4217F ALA 3.6 4.9 - - - +
4218F GLY* 5.2 2.2 - - - -
4237F THR 5.9 0.2 - - - +
4240F HIS* 4.0 16.2 - - + +
4241F ALA* 4.7 10.5 - - + +
4244F ILE* 3.5 33.4 - - + -
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Residues in contact with LEU4108 (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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4095F THR* 3.8 3.6 - - + -
4097F ALA* 5.2 0.4 - - - -
4102F ILE* 3.8 25.8 - - + -
4106F ASP* 4.8 0.4 - - + -
4107F VAL* 1.3 80.2 - - - +
4109F VAL* 1.3 63.5 + - - +
4110F THR* 3.9 3.8 + - - +
4152F HIS* 3.4 32.1 - - + +
4193F MET* 4.1 14.6 - - + +
4194F ASN* 3.4 44.4 + - + +
4215F MET* 4.4 0.7 - - - +
4216F VAL* 3.2 5.1 - - - -
4217F ALA* 2.8 38.1 + - - +
4219F VAL* 3.6 26.0 - - + -
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Residues in contact with VAL4109 (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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4107F VAL* 5.0 1.8 - - + -
4108F LEU* 1.3 74.8 - - - +
4110F THR* 1.3 65.2 + - - +
4137F THR* 3.6 30.1 - - + -
4140F LEU* 4.1 31.9 - - + +
4141F VAL* 4.1 16.8 - - + -
4144F ALA* 5.5 0.4 - - + -
4151F THR* 4.3 15.9 - - + -
4152F HIS 3.0 6.7 + - - +
4153F VAL* 3.4 12.0 - - + +
4154F GLY 3.1 24.4 + - - -
4193F MET* 3.2 4.8 - - - +
4215F MET 3.3 11.4 - - - +
4216F VAL* 4.6 9.6 - - + -
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Residues in contact with THR4110 (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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4108F LEU 4.5 2.8 + - - -
4109F VAL* 1.3 76.9 - - - +
4111F THR* 1.3 65.0 + - - +
4112F ALA* 3.4 25.4 - - - +
4113F SER* 4.2 4.7 - - - -
4132F ALA* 3.6 15.1 - - - +
4137F THR* 4.1 5.2 + - - -
4154F GLY 3.4 3.6 - - - -
4156F THR* 2.8 41.0 + - + +
4194F ASN* 4.8 0.3 + - - -
4199F SER* 4.7 1.6 - - - +
4203F LEU* 4.2 8.1 - - + -
4215F MET* 2.9 42.6 + - + +
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Residues in contact with THR4111 (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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6131B VAL* 3.9 20.6 - - - +
6132B ALA 4.9 5.8 + - - +
6134B PHE* 4.5 15.9 - - + +
4110F THR* 1.3 72.8 - - - +
4112F ALA* 1.3 66.4 + - - +
4131F VAL* 3.6 6.4 - - - +
4132F ALA* 2.8 33.6 + - - +
4137F THR* 4.7 9.8 + - + -
4153F VAL* 3.6 29.2 - - + +
4154F GLY* 2.8 28.6 + - - +
4155F VAL* 4.0 5.9 + - - +
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Residues in contact with ALA4112 (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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6129B PRO* 3.7 15.0 - - + -
6131B VAL* 3.5 30.7 - - + -
4110F THR* 3.4 7.1 - - - +
4111F THR* 1.3 80.5 + - - +
4113F SER* 1.3 61.9 + - - +
4130F ALA 3.1 15.7 - - - +
4131F VAL* 3.6 9.9 - - + -
4132F ALA 4.3 0.9 - - - +
4155F VAL* 3.3 25.1 - - - +
4156F THR 3.4 2.1 + - - -
4203F LEU* 4.3 0.2 - - - -
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Residues in contact with SER4113 (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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6127B GLU 3.9 0.2 - - - +
6129B PRO* 3.6 14.1 - - - +
4110F THR* 4.2 2.2 - - - -
4112F ALA* 1.3 75.9 - - - +
4114F VAL* 1.3 66.2 + - - +
4115F ARG* 3.3 4.7 + - - +
4130F ALA* 2.9 25.8 + - - +
4156F THR* 2.7 24.7 - - - +
4158F SER* 4.5 1.6 - - - -
4199F SER* 3.0 30.7 + - - -
4200F ALA* 3.5 17.2 + - - -
4203F LEU* 3.9 1.6 - - - +
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Residues in contact with VAL4114 (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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6127B GLU* 3.4 23.8 - - + +
6128B PHE* 3.9 19.3 - - + +
6129B PRO* 3.8 1.6 - - + -
4113F SER* 1.3 70.3 - - - +
4115F ARG* 1.3 61.9 + - - +
4116F LEU* 3.1 16.6 + - + +
4155F VAL* 3.8 21.8 - - + -
4156F THR 2.8 10.8 + - - +
4157F ALA* 4.0 14.4 - - + -
4158F SER* 3.1 21.3 + - - +
4187F TRP* 3.8 30.7 - - + -
4192F VAL* 4.1 12.8 - - + -
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Residues in contact with ARG4115 (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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6127B GLU* 2.9 35.9 + - - +
4113F SER 3.8 1.3 - - - +
4114F VAL* 1.3 67.7 - - - +
4116F LEU* 1.3 59.4 + - - +
4117F ASP* 3.2 15.3 + - - +
4120F SER* 2.9 40.6 + - - -
4121F LEU* 3.2 13.1 - - - +
4124F ALA 3.0 22.2 + - - -
4125F PRO 2.7 22.8 + - - -
4126F MET* 3.5 33.6 - - + +
4128F PHE* 2.9 29.0 + - - +
4130F ALA* 3.5 31.0 - - + +
4179F ARG* 5.1 0.2 + - - -
4200F ALA* 4.1 8.5 - - + -
4204F THR* 3.9 7.9 - - - +
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Residues in contact with LEU4116 (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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1122A HIS* 3.0 31.4 + - + -
6127B GLU* 4.2 6.7 - - + +
4114F VAL* 3.1 20.1 + - + +
4115F ARG* 1.3 76.6 - - - +
4117F ASP* 1.3 57.6 + - - +
4157F ALA* 4.0 18.4 - - + -
4158F SER 3.1 15.2 + - - +
4159F SER* 4.0 7.0 - - - -
4160F ASP 3.2 3.6 + - - -
4165F GLY 4.4 3.4 - - - +
4179F ARG* 3.5 29.2 - - - +
4180F PHE* 4.2 11.9 - - + -
4187F TRP* 3.7 42.8 - - + +
4195F TYR* 4.3 8.7 - - + -
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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