Contacts of the strand formed by residues 6151 - 6159 (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 THR6151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6107B VAL* 3.1 24.9 - - + +
6109B VAL* 3.9 21.3 - - + -
6141B VAL* 5.6 4.3 - - + +
6144B ALA* 3.1 28.1 + - + +
6149B ALA 2.7 16.5 + - - -
6150B THR* 1.3 72.3 - - - +
6152B HIS* 1.3 75.6 + - - +
6153B VAL* 4.3 11.1 - - + +
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Residues in contact with HIS6152 (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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6101B HIS* 3.9 27.1 + + - -
6102B ILE* 3.7 27.3 - - + +
6106B ASP* 3.6 26.7 + - + -
6107B VAL 2.9 5.7 + - - -
6108B LEU* 3.1 25.7 - - + -
6109B VAL 2.8 23.4 + - - -
6150B THR* 4.0 11.1 - - + +
6151B THR* 1.3 80.7 + - - +
6153B VAL* 1.3 62.7 + - - +
6193B MET* 3.6 12.9 - - + +
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Residues in contact with VAL6153 (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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6109B VAL* 3.2 22.2 - - + +
6111B THR* 3.6 22.0 - - + -
6137B THR* 5.4 0.2 - - + -
6141B VAL* 4.8 17.9 - - + -
6151B THR* 4.4 13.9 - - + +
6152B HIS* 1.3 79.2 - - - +
6154B GLY* 1.3 60.2 + - - +
6193B MET* 3.7 3.9 - - - +
4134F PHE* 4.1 23.8 - - + -
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Residues in contact with GLY6154 (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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6109B VAL 3.1 6.1 + - - -
6110B THR* 3.5 7.3 - - - +
6111B THR* 3.0 37.8 + - - +
6153B VAL* 1.3 76.8 - - - +
6155B VAL* 1.3 63.9 + - - -
6156B THR 3.9 0.3 + - - -
6191B GLY 5.9 0.2 - - - -
6193B MET* 3.1 14.4 - - - +
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Residues in contact with VAL6155 (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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6111B THR* 4.5 0.9 - - - +
6112B ALA 3.3 11.9 - - - +
6114B VAL* 3.7 28.3 - - + -
6154B GLY* 1.3 74.5 - - - -
6156B THR* 1.3 64.1 + - - +
6191B GLY 5.0 4.8 + - - +
6192B VAL* 3.6 11.2 - - + +
6193B MET* 2.9 33.2 + - - +
4128F PHE* 4.2 20.4 - - + -
4129F PRO* 3.8 11.9 - - + -
4131F VAL* 3.7 29.8 - - + -
4207F ALA* 4.9 7.4 - - + +
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Residues in contact with THR6156 (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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6110B THR* 2.7 35.0 + - - +
6112B ALA 3.0 6.3 + - - -
6113B SER* 3.1 7.8 - - - -
6114B VAL* 2.6 33.9 + - - +
6154B GLY 3.9 0.2 + - - -
6155B VAL* 1.3 75.4 - - - +
6157B ALA* 1.3 58.3 + - - +
6192B VAL* 4.0 2.9 - - - -
6193B MET* 4.0 3.6 - - - +
6194B ASN* 2.7 34.8 + - - +
6196B GLU* 3.4 33.0 - - + -
6199B SER* 4.0 5.2 - - - +
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Residues in contact with ALA6157 (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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6114B VAL* 3.9 12.8 - - + -
6116B LEU* 4.3 12.6 - - + -
6156B THR* 1.3 73.4 - - - +
6158B SER* 1.3 59.8 + - - +
6159B SER 3.6 1.4 + - - -
6187B TRP* 4.5 7.2 - - + -
6192B VAL* 3.6 14.2 - - + +
6194B ASN 2.9 18.1 + - - +
6195B TYR* 3.3 28.3 - - + -
6196B GLU 3.2 21.7 + - - +
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Residues in contact with SER6158 (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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6113B SER* 4.3 2.0 - - - -
6114B VAL 3.2 8.8 + - - -
6116B LEU* 3.1 31.4 + - - +
6117B ASP* 3.6 4.5 + - - +
6156B THR 3.6 1.6 + - - -
6157B ALA* 1.3 69.6 - - - +
6159B SER* 1.3 58.4 + - - +
6196B GLU* 2.7 28.5 + - - -
6197B MET 3.8 1.9 - - - -
6198B GLU* 3.5 11.1 + - - -
6199B SER* 3.5 3.6 - - - -
6200B ALA* 3.2 37.9 + - - +
6201B THR* 4.6 0.5 + - - +
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Residues in contact with SER6159 (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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6116B LEU* 3.5 12.3 - - - -
6117B ASP* 4.9 0.8 - - - +
6157B ALA 3.6 3.2 + - - -
6158B SER* 1.3 74.3 - - - +
6160B ASP* 1.3 62.7 + - - +
6161B THR* 2.6 34.7 + - - -
6165B GLY* 3.4 12.7 - - - -
6166B GLN* 3.9 20.0 - - - -
6195B TYR* 5.0 1.1 - - - -
6196B GLU 2.9 6.4 + - - -
6197B MET* 3.3 28.2 - - - +
3122D HIS* 3.3 12.1 - - - -
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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