Contacts of the strand formed by residues 170 - 175 (chain C) in PDB entry 2W4T
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 170 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ALA* 3.0 13.1 - - + +
162C ASN* 2.5 39.6 + - - +
163C MET* 2.1 52.3 - - + +
168C GLU* 2.8 22.1 + - - +
169C ASN* 1.3 75.3 - - - +
171C SER* 1.3 73.2 + - - +
248C ARG* 3.6 5.9 + - - -
455C TYR 3.1 0.6 + - - -
456C ILE* 3.3 9.8 - - + -
457C GLY 3.6 11.1 + - - -
663C THR* 4.6 0.7 - - - -
664C HIS* 2.7 35.5 - - - +
666C HIS* 3.4 13.4 + - + +
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Residues in contact with SER 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C GLN* 1.3 84.9 + - - +
172C CYS* 1.3 57.2 + - - +
173C LEU* 4.2 0.9 - - - -
246C PHE* 5.8 0.4 - - - -
248C ARG* 2.9 21.4 + - - -
456C ILE* 3.5 7.2 - - - -
457C GLY 3.6 4.3 - - - -
660C LEU* 4.3 13.9 - - - +
663C THR* 3.4 27.1 - - - +
664C HIS 3.6 1.4 + - - -
665C PRO* 3.3 6.1 - - - +
666C HIS* 2.2 51.9 + - - -
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Residues in contact with CYS 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C VAL* 5.6 2.0 - - + -
171C SER* 1.3 74.0 - - - +
173C LEU* 1.3 63.2 + - - +
174C ILE* 3.7 12.0 + - + -
189C VAL* 4.7 12.8 - - + -
456C ILE* 5.3 1.6 - - - -
457C GLY 3.3 3.6 + - - -
458C VAL* 3.2 46.2 - - - -
459C LEU* 3.0 20.3 + - - +
666C HIS* 3.1 24.0 - - + +
668C VAL* 5.0 7.6 - - + -
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Residues in contact with LEU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C SER* 4.2 1.3 + - - -
172C CYS* 1.3 73.2 - - - +
174C ILE* 1.3 59.7 + - - +
175C THR* 3.7 4.5 - - + -
459C LEU* 2.7 52.5 - - + +
461C ILE* 4.6 9.9 - - + -
484C LEU* 4.1 20.9 - - + -
487C PHE* 3.9 27.4 - - + -
660C LEU* 3.5 26.9 - - + -
665C PRO* 6.1 5.5 - - + +
666C HIS 3.2 6.8 + - - +
667C PHE* 3.0 36.5 - - + -
668C VAL* 3.0 10.9 + - - -
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Residues in contact with ILE 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C CYS* 4.0 23.8 - - - -
173C LEU* 1.3 65.1 - - - +
175C THR* 1.3 57.8 + - - +
181C GLY 4.4 0.4 - - - +
182C LYS* 2.4 75.4 - - + +
185C ASN* 5.1 6.3 - - + +
186C THR* 3.3 25.8 - - + +
189C VAL* 5.6 2.7 - - + -
458C VAL* 4.3 1.8 - - + -
459C LEU 3.4 19.3 + - - +
460C ASP* 4.3 1.6 - - - -
461C ILE* 4.9 1.4 + - - +
484C LEU* 5.2 1.3 - - - +
668C VAL* 2.3 38.4 - - + -
670C CYS* 5.3 0.9 - - + -
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Residues in contact with THR 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C LEU* 4.2 3.1 - - + +
174C ILE* 1.3 78.2 - - - +
176C GLY* 1.3 53.9 + - - +
182C LYS* 3.9 6.1 - - - -
461C ILE 5.6 0.2 - - - -
484C LEU* 2.9 44.4 - - + -
667C PHE* 2.0 53.7 - - + -
668C VAL 2.8 9.7 + - - -
669C ARG* 3.5 2.5 - - - +
670C CYS* 2.5 39.6 + - - +
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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