Contacts of the strand formed by residues 176 - 183 (chain A) in PDB entry 4D1Q
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 SER 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ALA* 1.3 72.7 + - - +
177A ALA* 1.3 59.7 + - - +
196A LEU* 3.2 5.5 - - - +
197A HIS* 2.6 48.0 + - - +
243A ILE* 4.3 1.1 - - - -
244A LYS* 3.0 17.5 + - - +
563A SER* 4.0 2.7 - - - -
564A ILE* 3.1 48.7 - - - +
565A PRO* 3.7 9.2 - - - -
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 1.3 76.7 - - - +
178A THR* 1.3 57.7 + - - +
194A VAL* 4.8 3.4 - - + -
195A THR 2.9 16.6 - - - +
196A LEU* 4.4 8.5 - - + -
197A HIS* 4.2 0.9 - - - -
232A PHE* 4.5 5.4 - - + -
243A ILE* 3.9 8.5 - - + +
244A LYS 2.6 10.5 + - - -
245A PHE* 3.1 34.4 - - + -
246A VAL* 2.8 31.0 + - - +
565A PRO* 5.2 0.4 - - - +
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Residues in contact with THR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ALA* 1.3 74.7 - - - +
179A ILE* 1.3 62.0 + - - +
194A VAL* 3.4 2.4 - - - -
195A THR* 2.3 56.2 + - - +
197A HIS* 4.1 1.6 - - - +
245A PHE* 5.1 0.4 - - - -
246A VAL* 3.1 36.1 - - + +
565A PRO* 4.0 22.4 - - + -
567A SER 4.4 0.9 - - - +
568A SER* 4.2 12.3 - - - -
570A ALA* 3.5 1.8 - - + +
571A SER* 3.0 23.8 + - - -
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Residues in contact with ILE 179 (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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178A THR* 1.3 82.2 - - - +
180A ASP* 1.3 63.4 + - - +
192A LEU* 3.7 13.0 - - + -
193A GLY 3.2 14.1 - - - +
194A VAL* 3.8 23.8 - - + -
224A ILE* 4.6 8.1 - - + -
228A LEU* 4.2 17.7 - - + -
245A PHE* 4.4 9.9 - - + -
246A VAL 3.7 3.0 + - - -
247A THR* 3.1 22.5 + - - +
253A VAL* 3.6 22.7 - - + +
256A SER* 4.5 4.9 - - - +
257A LEU* 3.6 31.2 - - + -
568A SER* 4.9 1.7 - - - -
571A SER* 3.3 3.5 - - - -
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Residues in contact with ASP 180 (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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179A ILE* 1.3 75.0 - - - +
181A LEU* 1.3 81.5 + - - +
192A LEU* 3.2 7.7 - - - +
193A GLY 3.1 27.1 + - - -
248A ASP* 3.1 27.3 - - - +
253A VAL* 5.3 3.6 - - - -
268A HIS* 4.2 2.1 + - - -
568A SER* 4.0 10.5 + - - -
571A SER* 3.5 10.9 + - - -
572A GLU* 2.8 25.7 - - - +
575A PHE* 3.3 24.8 - - + -
16D G 5.0 1.1 - - - +
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Residues in contact with LEU 181 (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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180A ASP* 1.3 90.3 + - - +
182A TRP* 1.3 63.6 + - - +
190A ASN* 4.5 11.2 - - - +
191A PHE 3.2 15.9 - - - +
192A LEU* 3.8 24.2 - - + -
214A LEU* 4.0 16.6 - - + -
219A SER* 4.5 11.9 - - - +
224A ILE* 3.8 19.5 - - + -
252A ASN* 4.0 12.3 - - - +
253A VAL* 3.6 31.2 - - + -
575A PHE* 3.8 4.6 - - - -
16D G 5.0 4.0 + - - -
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Residues in contact with TRP 182 (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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181A LEU* 1.3 73.3 - - - +
183A THR* 1.3 81.6 + - - +
184A ASP* 3.6 30.3 - - + -
185A ASN* 6.1 1.1 - - - -
190A ASN* 3.2 5.3 + - - +
191A PHE* 2.6 63.4 + + + +
211A LEU* 4.5 4.7 - - + -
575A PHE* 3.1 65.9 + + + +
578A ALA* 4.0 23.3 - - + -
579A GLY* 4.2 13.9 - - - -
582A ILE* 4.2 9.2 - - + -
15D T 4.0 8.5 + - - -
16D G 3.8 22.7 + - - -
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Residues in contact with THR 183 (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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182A TRP* 1.3 94.1 + - - +
184A ASP* 1.3 69.7 + - - +
185A ASN* 5.2 1.2 - - - +
188A LYS* 4.2 10.8 - - + +
189A ARG 3.3 18.4 - - - +
190A ASN* 3.0 33.0 + - + +
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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