Contacts of the strand formed by residues 176 - 183 (chain C) in PDB entry 3Q29
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 LYS 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A THR* 5.8 1.2 + - - -
247A VAL* 5.5 8.5 - - + +
323A GLU* 3.6 30.1 - - - +
172C TYR* 3.4 11.2 - - - -
173C GLU 2.9 35.8 + - - +
174C ASN* 4.2 24.4 + - - +
175C GLY* 1.3 81.0 - - - +
177C TYR* 1.3 68.5 + - - +
178C ASP* 3.5 9.7 + - - +
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Residues in contact with TYR 177 (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 PHE* 3.4 27.1 - - + -
171C LYS 3.2 7.0 - - - +
172C TYR* 3.5 34.0 - + + -
176C LYS* 1.3 80.5 - - - +
178C ASP* 1.3 59.0 + - - +
179C ILE* 2.9 19.9 + - - +
330C ILE* 4.0 15.4 + - - +
331C MET 4.5 1.2 + - - -
332C PRO* 3.4 48.9 - - + +
333C ASN* 5.0 3.4 - - - -
334C ILE* 4.0 32.5 - - + +
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Residues in contact with ASP 178 (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 PHE* 4.0 5.4 - - - -
171C LYS* 2.9 19.8 + - + +
173C GLU* 5.5 8.5 - - + -
176C LYS* 3.5 14.0 + - - +
177C TYR* 1.3 67.1 - - - +
179C ILE* 1.3 54.1 + - - +
180C LYS* 2.8 31.2 + - - +
181C ASP* 3.0 41.8 + - + +
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Residues in contact with ILE 179 (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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322A MET* 6.2 3.6 - - + -
323A GLU* 6.0 13.5 - - + +
326A GLN* 4.5 18.2 - - + +
170C PHE* 4.0 18.2 - - - -
177C TYR 2.9 14.1 + - - +
178C ASP* 1.3 69.1 + - - +
180C LYS* 1.3 59.4 + - + +
334C ILE* 4.1 12.3 - - + -
336C GLN* 3.1 38.3 - - + +
369C SER 4.9 0.7 - - - +
370C SER* 2.7 24.8 + - - -
375C PHE* 5.5 6.7 - - + -
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Residues in contact with LYS 180 (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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312A LEU 5.0 1.8 + - - -
313A ALA* 3.2 32.5 + - + +
315A ASP 5.1 1.0 + - - -
316A PRO* 5.7 0.8 - - - +
319A ALA* 3.9 29.2 - - - +
178C ASP* 2.9 10.3 + - - +
179C ILE* 1.3 93.9 - - + +
181C ASP* 1.3 60.9 + - - +
182C VAL* 3.5 5.8 + - - +
366C GLN* 5.2 4.7 + - - -
370C SER* 3.1 19.5 + - - +
371C SER* 5.9 5.2 - - - +
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Residues in contact with ASP 181 (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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168C TYR* 2.8 24.0 + - - -
170C PHE* 3.7 2.9 - - - -
171C LYS* 3.0 60.2 + - + +
178C ASP* 3.0 26.9 + - - +
180C LYS* 1.3 75.9 - - - +
182C VAL* 1.3 60.4 + - - +
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Residues in contact with VAL 182 (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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168C TYR* 3.9 4.3 + - - -
169C ALA 3.2 6.3 - - - +
170C PHE* 3.3 35.0 - - + -
180C LYS 3.5 4.4 + - - -
181C ASP* 1.3 73.9 + - - +
183C GLY* 1.3 61.5 + - - +
184C VAL* 3.5 38.1 + - + -
185C ASP 4.7 0.7 + - - -
186C ASN 5.7 0.3 + - - -
340C PHE* 5.0 1.8 - - + -
366C GLN* 3.3 35.1 + - + +
369C SER* 3.9 11.7 - - - +
370C SER* 3.5 24.7 - - - +
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Residues in contact with GLY 183 (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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159C TRP* 4.7 0.3 - - - -
167C GLY* 3.5 9.0 - - - -
168C TYR* 2.7 62.0 + - - +
169C ALA 3.0 12.3 + - - -
182C VAL* 1.3 71.0 - - - +
184C VAL* 1.3 57.5 + - - +
185C ASP 3.4 2.9 - - - -
186C ASN* 3.7 9.3 + - - +
189C ALA* 4.3 0.2 - - - +
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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