Contacts of the strand formed by residues 173 - 179 (chain J) in PDB entry 1O19
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 GLN 173 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162J ALA* 3.6 24.5 - - + +
165J PHE* 3.7 9.0 + - - +
166J MET* 3.6 14.5 - - + +
169J ASP* 5.2 0.7 - - - +
171J GLU* 2.9 31.1 + - - +
172J ASN* 1.3 79.7 + - - +
174J SER* 1.3 58.5 + - - +
458J PHE* 3.2 7.6 + - - +
459J ILE* 3.6 22.9 - - + -
460J GLY* 3.0 21.2 + - - -
667J THR* 3.0 17.1 + - - +
668J HIS* 2.6 39.1 + - - +
670J HIS* 3.2 25.5 + - + -
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Residues in contact with SER 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J GLN* 1.3 73.9 - - - +
175J ILE* 1.3 59.1 - - - +
176J LEU* 3.3 12.1 - - - +
249J PHE* 5.5 1.3 - - - -
460J GLY* 3.0 14.8 - - - -
462J LEU* 6.3 0.4 - - - -
490J PHE* 5.1 0.3 - - - -
664J LEU* 4.7 14.5 + - - +
667J THR* 2.9 26.9 - - - +
668J HIS 3.2 2.2 + - - -
669J PRO* 3.1 16.8 - - - +
670J HIS* 2.7 38.6 + - - +
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Residues in contact with ILE 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J ILE* 4.0 20.9 - - + -
159J SER* 4.8 1.8 - - - -
162J ALA* 4.5 10.1 - - + -
174J SER* 1.3 80.3 - - - +
176J LEU* 1.3 64.0 + - - +
177J ILE* 3.5 26.7 - - + -
192J VAL* 4.7 10.3 - - + -
196J PHE* 4.2 18.8 - - + -
459J ILE* 4.2 22.4 - - + -
460J GLY 2.7 9.1 + - - +
461J VAL* 3.7 9.8 - - + -
462J LEU* 3.0 26.0 + - - +
670J HIS* 2.9 7.0 - - + -
672J VAL* 3.8 20.9 - - + -
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Residues in contact with LEU 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174J SER* 3.3 24.5 - - - +
175J ILE* 1.3 79.8 - - - +
177J ILE* 1.4 60.2 - - - +
178J THR* 5.9 0.2 - - - +
462J LEU* 3.6 32.1 - - + -
487J LEU* 4.6 10.8 - - + -
490J PHE* 4.5 10.1 - - + -
664J LEU* 4.4 17.0 - - + -
669J PRO* 4.5 2.9 - - + -
670J HIS 2.7 27.9 + - - +
671J PHE* 4.2 23.1 - - + -
672J VAL 2.8 26.8 + - - +
673J ARG* 3.0 17.5 + - - +
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Residues in contact with ILE 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J ILE* 6.2 0.2 - - + -
175J ILE* 3.5 23.6 - - + -
176J LEU* 1.4 70.4 - - - +
178J THR* 1.3 70.7 + - - +
185J LYS* 3.6 22.8 - - + +
188J ASN* 4.8 4.0 - - + -
189J THR* 4.4 22.2 - - + +
192J VAL* 4.4 10.5 - - + -
461J VAL* 4.0 22.0 - - + -
462J LEU* 2.9 21.7 + - - +
463J ASP* 4.0 2.4 - - - -
464J ILE* 3.7 13.2 + - - +
672J VAL* 3.4 24.2 - - + +
674J CYS* 3.5 27.6 - - - -
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Residues in contact with THR 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J LEU* 5.4 0.5 - - - +
177J ILE* 1.3 82.1 + - - +
179J GLY* 1.4 61.4 + - - +
185J LYS* 4.3 3.6 - - - -
462J LEU* 5.7 2.8 - - - +
464J ILE* 3.5 16.8 + - - +
465J ALA 4.2 2.9 + - - -
466J GLY* 4.6 11.4 - - - -
484J ASN* 4.0 14.0 + - - +
487J LEU* 5.4 4.2 - - - +
672J VAL 3.3 4.4 + - - -
673J ARG* 3.6 39.5 + - - +
674J CYS* 2.9 26.2 + - - +
697J CYS 5.8 1.1 - - - +
698J ASN* 4.8 12.3 + - - +
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Residues in contact with GLY 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J THR* 1.4 79.6 - - - +
180J GLU* 1.3 63.3 + - - -
181J SER 4.0 0.2 + - - -
183J ALA* 4.1 4.9 - - - -
185J LYS* 2.9 25.1 - - - +
464J ILE 4.3 1.4 + - - -
465J ALA* 4.2 1.7 - - - +
466J GLY* 3.8 18.1 + - - +
674J CYS* 3.7 15.0 - - - -
698J ASN* 5.4 3.6 - - - -
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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