Contacts of the strand formed by residues 169 - 177 (chain A) in PDB entry 4QY2
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 HIS 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 4.1 21.2 - - + +
161A TYR* 2.5 34.1 + - + +
163A ASN* 3.2 24.3 + - - +
164A THR 5.4 0.4 - - - -
165A ASP* 3.1 31.8 + - + +
167A ALA 3.3 10.5 - - - -
168A GLU* 1.3 85.2 - - - +
170A LEU* 1.3 61.0 - - - +
171A ILE 3.6 0.9 + - - -
229A LEU* 3.1 6.2 - - - -
230A VAL* 2.6 41.5 + - + +
250A VAL* 4.0 11.0 - - + +
251A SER 3.6 7.6 - - - +
252A LYS* 3.9 16.7 - - + +
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.1 14.6 - - + -
98A LEU* 3.7 24.5 - - + -
101A LYS* 4.5 9.9 - - + -
168A GLU 4.3 0.8 + - - -
169A HIS* 1.3 69.7 - - - +
171A ILE* 1.3 63.8 + - - +
172A MET* 3.7 28.2 + - + +
227A TRP* 3.8 19.5 - - + -
228A THR 3.5 7.0 - - - +
229A LEU* 3.7 23.3 - - + +
250A VAL* 3.6 2.1 - - - +
251A SER* 2.8 47.7 + - - +
252A LYS* 4.9 0.6 - - - +
253A LEU* 4.5 18.6 - - + +
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Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A THR* 5.2 0.2 - - + -
161A TYR* 4.4 8.7 - - + -
169A HIS 3.6 0.8 + - - -
170A LEU* 1.3 75.0 - - - +
172A MET* 1.3 71.0 + - - +
173A TRP* 3.7 16.9 - - + -
227A TRP* 3.2 23.4 - - - +
228A THR 3.0 12.0 + - - +
230A VAL* 3.5 27.6 - - + -
236A ILE* 4.1 19.1 - - + -
238A PHE* 3.6 30.1 - - + -
247A PRO* 3.9 11.0 - - + -
250A VAL* 3.7 29.6 - - + +
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Residues in contact with MET 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE* 4.7 4.9 - - + +
60A LEU* 3.8 32.5 - - + +
61A ILE* 3.8 27.1 - - + -
92A THR* 4.1 9.9 - - + +
98A LEU* 3.8 28.9 - - + -
142A LEU* 3.6 8.5 - - + +
170A LEU* 3.7 9.8 + - + +
171A ILE* 1.3 75.7 - - - +
173A TRP* 1.3 63.8 + - - +
225A PHE* 3.9 23.1 - - + -
226A HIS 3.2 7.6 - - - +
227A TRP* 3.6 17.5 - - + -
247A PRO* 3.2 25.9 - - - +
249A ARG 5.3 2.7 + - - +
250A VAL* 5.4 0.8 - - - +
251A SER* 6.1 0.4 - - - +
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Residues in contact with TRP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 4.2 4.0 - - - -
171A ILE* 3.7 25.8 - - + -
172A MET* 1.3 82.1 - - - +
174A GLY* 1.3 62.9 + - - +
175A ILE* 4.2 7.9 - - + -
197A VAL* 4.0 12.5 - - + +
202A TYR* 3.4 41.3 - + - -
206A PHE* 3.6 21.7 - + - -
225A PHE* 3.3 10.0 - - - +
226A HIS* 2.7 55.7 + - + +
227A TRP* 3.8 12.6 - - - -
228A THR* 3.9 14.8 - - - -
236A ILE* 4.7 1.3 - - + -
238A PHE* 3.6 36.3 - + + -
244A LEU* 4.0 11.0 - - + -
245A ILE 3.6 13.5 - - - +
247A PRO* 4.0 5.6 - - + -
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Residues in contact with GLY 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A TRP* 1.3 75.2 - - - +
175A ILE* 1.3 69.3 + - - +
223A ILE* 4.0 9.4 - - - -
224A ASP 3.1 9.9 - - - -
225A PHE* 4.0 4.9 - - - -
244A LEU* 3.6 2.3 - - - +
245A ILE* 2.6 51.5 + - - +
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A TRP* 4.2 7.6 - - + -
174A GLY* 1.3 83.9 - - - +
176A HIS* 1.3 62.4 + - - +
177A HIS* 3.5 31.7 - - + +
195A ILE* 3.7 28.5 - - + -
206A PHE* 3.7 40.2 - - + -
208A PRO* 4.0 22.2 - - + -
223A ILE* 3.4 3.5 - - - -
224A ASP* 2.8 33.8 + - + +
226A HIS* 4.1 15.9 - - + +
243A GLY 3.3 5.6 - - - +
244A LEU* 4.4 1.1 - - - -
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Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TYR* 3.3 22.1 + - - -
144A TRP* 3.5 25.2 - + - -
174A GLY 4.2 0.4 - - - -
175A ILE* 1.3 71.8 - - - +
177A HIS* 1.3 62.3 + - - +
178A PRO* 3.2 42.9 - - + +
183A GLU* 3.6 16.1 + - - -
187A LEU* 3.7 11.0 - - + -
188A TYR* 2.7 26.0 + - - +
208A PRO* 3.4 20.4 - - - +
221A GLY* 4.6 0.2 - - - -
222A ARG 3.4 17.9 - - - -
223A ILE* 4.0 9.2 - - + -
243A GLY* 2.7 16.8 + - - +
245A ILE* 4.3 14.5 - - + +
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Residues in contact with HIS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE* 3.5 30.9 + - + +
176A HIS* 1.3 73.6 - - - +
178A PRO* 1.3 59.5 - - - +
207A VAL 3.7 14.1 - - - -
208A PRO* 3.6 6.2 - - + +
209A VAL* 2.9 39.2 + - + +
213A ARG* 2.8 34.9 + - - +
222A ARG* 2.7 27.4 + - + +
224A ASP* 3.5 14.6 + - - +
226A HIS* 5.9 1.0 - - - -
203C ARG* 3.0 44.5 + - - +
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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