Contacts of the strand formed by residues 172 - 179 (chain I) in PDB entry 6G2T
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 ILE 172 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164I GLY* 3.5 35.9 - - - +
165I GLU 3.7 13.7 - - - +
166I VAL* 3.9 14.8 - - + -
171I SER* 1.3 75.5 - - - +
173I THR* 1.3 68.8 + - - +
174I PHE* 3.5 23.1 + - + -
224I LEU 4.0 1.0 - - - +
225I HIS 4.0 0.2 - - - -
226I ILE* 2.9 55.9 + - + +
254I LEU* 3.9 20.2 - - + -
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Residues in contact with THR 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171I SER* 5.6 0.7 - - - -
172I ILE* 1.3 80.2 - - - +
174I PHE* 1.3 77.8 + - - +
175I SER* 5.4 1.8 - - - -
223I GLU* 4.6 12.3 - - + +
224I LEU 3.5 6.1 - - - +
225I HIS* 3.1 40.4 + - + +
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Residues in contact with PHE 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I PRO* 5.3 3.4 - - + -
162I GLN 2.9 32.5 - - - -
163I ASP 3.9 0.2 - - - -
164I GLY* 3.4 22.2 - - - -
172I ILE* 3.5 30.7 - - + -
173I THR* 1.3 80.1 - - - +
175I SER* 1.3 60.1 + - - +
191I TRP* 4.2 6.8 - - + -
222I PHE 4.1 0.2 - - - +
223I GLU* 3.4 2.4 - - - +
224I LEU* 2.7 58.3 + - + +
226I ILE* 4.4 8.1 - - + -
252I PHE* 3.7 32.8 - + + -
253I ASN 4.7 0.4 - - - -
254I LEU* 3.6 27.4 - - + -
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Residues in contact with SER 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159I MET* 4.5 18.5 - - - +
160I ARG 4.2 2.9 - - - +
161I PRO* 3.6 20.4 - - - +
162I GLN 4.9 1.0 + - - +
173I THR* 4.4 2.4 + - - -
174I PHE* 1.3 77.0 - - - +
176I ALA* 1.3 61.2 + - - +
191I TRP* 4.6 3.8 - - - -
221I LEU* 3.8 14.4 - - - +
222I PHE 3.2 12.8 - - - -
223I GLU* 3.7 18.6 - - - -
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Residues in contact with ALA 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I PHE* 5.0 10.3 - - + -
159I MET* 3.5 12.8 - - - +
161I PRO* 4.0 20.9 - - + -
175I SER* 1.3 76.0 - - - +
177I ARG* 1.3 64.2 + - - +
178I VAL* 4.4 0.4 + - - -
191I TRP* 4.7 2.0 - - + -
220I TYR 3.7 0.7 - - - +
221I LEU* 3.7 2.5 - - - +
222I PHE* 2.9 39.9 + - + +
239I CYS* 4.3 15.3 - - - -
241I VAL* 5.4 3.4 - - + -
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Residues in contact with ARG 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I PHE* 3.3 8.8 - - - +
158I VAL* 2.7 42.6 + - + +
159I MET* 3.2 34.4 + - + +
176I ALA* 1.3 72.7 - - - +
178I VAL* 1.3 60.7 + - - +
217I SER* 5.3 4.6 + - - -
219I VAL* 3.5 32.1 - - + +
220I TYR 3.2 4.7 - - - +
221I LEU* 3.6 36.8 - - + +
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Residues in contact with VAL 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156I LEU* 3.3 31.0 - - + +
157I PHE* 4.1 5.4 - - + -
158I VAL* 4.2 2.2 - - - -
176I ALA 5.3 0.4 - - - -
177I ARG* 1.3 79.2 - - - +
179I ALA* 1.3 73.7 + - - +
180I GLY 3.7 0.3 + - - -
187I PRO* 3.8 25.1 - - + -
219I VAL* 3.7 1.3 - - - -
220I TYR* 2.8 40.3 + - + +
222I PHE* 4.1 11.9 - - + -
241I VAL* 3.6 34.5 - - + -
243I THR* 4.5 5.6 - - + -
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Residues in contact with ALA 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156I LEU* 4.1 4.7 + - - +
158I VAL* 3.6 23.0 - - + +
178I VAL* 1.3 86.2 - - - +
180I GLY* 1.3 63.3 + - - +
187I PRO* 5.0 2.1 - - - +
218I LYS 3.9 7.4 - - - +
219I VAL* 4.7 4.0 - - + +
220I TYR* 4.7 0.2 - - - -
243I THR* 5.8 1.0 - - - +
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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