Contacts of the strand formed by residues 6050 - 6057 (chain B) 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 PHE6050 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6008B HIS* 4.0 14.1 - + + -
6009B LEU* 3.4 38.3 - - + +
6045B ALA 4.3 0.3 - - - -
6046B SER* 3.5 2.9 + - - -
6047B HIS* 2.8 39.1 + - - +
6048B ARG* 3.1 9.1 - - + -
6049B GLU* 1.3 81.2 - - + +
6051B THR* 1.3 61.2 + - - +
6052B SER* 3.8 2.9 + - - -
6065B CYS* 4.8 2.7 - - - -
6066B SER* 3.4 18.6 - - - +
6067B THR 3.6 12.1 - - - -
6073B SER* 3.1 44.0 - - - -
6076B ILE* 3.6 18.6 - - + -
6077B ALA* 4.0 7.6 - - + -
3069D ILE* 3.7 24.0 - - + -
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Residues in contact with THR6051 (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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6028B PRO* 3.5 39.2 + - - +
6031B VAL* 2.8 40.6 - - + +
6032B GLU 5.5 0.2 - - - +
6043B LYS* 5.5 3.1 - - - -
6045B ALA 3.5 10.8 - - - +
6046B SER* 3.2 21.4 + - - -
6048B ARG 5.0 1.7 + - - -
6050B PHE* 1.3 71.4 + - - +
6052B SER* 1.3 60.2 + - - +
6053B TRP* 4.2 12.1 - - + +
6065B CYS* 3.5 0.4 - - - -
6066B SER* 2.9 17.7 + - - +
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Residues in contact with SER6052 (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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6009B LEU* 4.6 2.4 + - - -
6011B LEU* 3.4 38.8 - - - +
6044B LEU* 2.8 33.8 + - - +
6045B ALA* 3.0 22.2 + - - +
6050B PHE 3.8 2.4 + - - -
6051B THR* 1.3 74.5 - - - +
6053B TRP* 1.3 60.2 + - - +
6063B ILE* 5.0 2.9 - - - -
6064B VAL 3.3 5.6 - - - -
6065B CYS* 3.9 21.3 - - - +
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Residues in contact with TRP6053 (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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6031B VAL* 3.5 29.3 - - + +
6032B GLU* 3.7 46.6 + - - +
6035B ALA* 3.9 18.2 - - + -
6041B PRO* 3.4 40.4 - - + -
6042B VAL 3.4 21.8 - - - -
6043B LYS* 3.4 41.2 - - + +
6044B LEU* 4.1 3.6 - - - +
6051B THR* 4.2 10.1 - - + +
6052B SER* 1.3 79.9 - - - +
6054B ARG* 1.3 60.5 + - - +
6063B ILE* 3.8 6.4 - - - +
6064B VAL* 2.8 30.3 + - + +
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Residues in contact with ARG6054 (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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6015B ASP* 2.7 42.8 + - - +
6016B LEU 4.2 4.0 - - - +
6017B GLN* 3.7 33.8 + - - +
6040B LYS 3.6 2.1 + - - +
6041B PRO* 3.2 4.3 - - - +
6042B VAL* 2.7 71.3 + - + +
6044B LEU* 3.3 30.9 - - + +
6053B TRP* 1.3 76.0 - - - +
6055B ALA* 1.3 73.0 + - - +
6056B GLU* 6.1 0.4 - - + -
6061B ALA* 4.8 4.5 - - + -
6062B VAL 3.7 7.9 - - - +
6063B ILE* 4.3 7.2 - - + -
6064B VAL* 5.7 0.4 - - - -
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Residues in contact with ALA6055 (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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6035B ALA* 4.1 13.0 - - + +
6038B MET* 3.8 26.9 - - + -
6039B ASP 3.4 13.0 - - - +
6040B LYS 3.9 4.0 - - - -
6041B PRO* 4.2 2.7 - - + -
6054B ARG* 1.3 80.3 - - - +
6056B GLU* 1.3 66.3 + - - +
6061B ALA* 3.3 7.3 - - - +
6062B VAL* 2.8 37.9 + - + +
6064B VAL* 5.2 0.7 - - + -
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Residues in contact with GLU6056 (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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6038B MET* 3.6 4.0 - - - +
6039B ASP* 2.8 48.2 + - + +
6040B LYS* 2.6 43.8 + - + +
6054B ARG* 6.1 0.9 - - + -
6055B ALA* 1.3 80.0 - - - +
6057B LEU* 1.3 60.6 + - - +
6058B ASP 4.2 0.4 - - - -
6059B GLY* 3.1 33.1 - - - +
6060B LYS 3.2 10.8 - - - +
6061B ALA* 4.1 9.9 + - + +
6062B VAL* 4.2 2.0 - - - -
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Residues in contact with LEU6057 (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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6037B LEU 5.1 1.3 - - - +
6038B MET* 3.7 34.3 - - + -
6039B ASP* 4.8 2.2 - - - +
6056B GLU* 1.3 74.7 - - - +
6058B ASP* 1.3 73.6 + - - +
6059B GLY 3.2 0.2 - - - -
6060B LYS* 2.7 19.0 + - - +
6062B VAL* 4.2 9.2 - - + +
6246B VAL* 3.7 19.7 - - + +
6249B ALA* 3.9 11.2 - - + -
6250B ARG* 3.2 56.1 - - + +
6253B LEU* 3.5 20.0 - - + +
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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