Contacts of the strand formed by residues 170 - 178 (chain B) in PDB entry 3GG0
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B HIS* 3.5 8.9 - - - +
164B LEU 2.6 38.2 + - - +
165B PRO 4.3 0.2 - - - -
167B GLN* 4.3 9.2 - - - +
169B CYS* 1.3 75.5 - - - +
171B PHE* 1.3 68.9 + - - +
191B ILE* 3.5 2.4 - - - +
192B ARG* 2.6 35.7 + - + +
193B SER 3.1 17.7 + - - +
194B PRO* 3.1 28.9 + - - +
196B GLY* 4.0 6.9 - - - +
388B LEU* 3.7 17.0 - - + +
389B ASN* 2.9 23.3 + - - +
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B CYS* 4.2 7.2 - - - -
170B GLN* 1.3 84.2 - - - +
172B ALA* 1.3 63.3 + - - +
189B ALA* 3.9 21.8 - - + -
190B LEU 3.3 5.6 - - - -
191B ILE* 3.5 42.2 - - + -
218B SER* 3.1 41.1 - - - -
219B LYS* 4.1 7.9 - - + -
221B TYR* 4.0 9.4 - - + -
222B ALA* 3.5 30.3 - - + -
225B LEU* 3.9 18.5 - - + +
388B LEU* 3.8 5.1 - - - +
389B ASN* 2.9 30.8 + - - +
501B C2E 4.1 8.1 - - - -
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B PHE* 1.3 73.0 - - - +
173B LEU* 1.3 61.2 + - - +
188B GLU 3.4 2.4 - - - +
189B ALA* 3.6 2.3 - - - -
190B LEU* 2.7 38.3 + - + +
192B ARG* 3.8 38.4 - - + +
386B PRO* 3.9 13.9 - - + -
387B CYS 3.3 15.3 - - - +
388B LEU* 4.0 5.2 - - + +
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B PHE* 5.5 0.2 - - + -
172B ALA* 1.3 74.6 - - - +
174B GLN* 1.3 59.9 + - - +
175B ALA 4.3 0.2 - - - -
187B PHE* 4.3 22.4 - - + -
188B GLU 3.4 16.4 - - - +
189B ALA* 3.9 19.3 - - + -
222B ALA 6.0 0.4 - - - +
225B LEU* 3.9 25.6 - - + -
226B ALA* 5.6 6.1 - - + -
229B LEU* 3.6 30.3 - - + -
236B LEU* 4.3 14.6 - - + -
384B SER* 5.0 0.7 + - - -
385B ARG 3.7 2.9 - - - +
386B PRO* 3.4 1.5 - - - +
387B CYS* 2.8 35.3 + - - +
390B GLY 3.4 16.6 - - - +
391B ILE* 4.7 5.4 - - + -
392B GLY 5.0 2.1 + - - -
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Residues in contact with GLN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ALA 4.2 0.4 + - - -
173B LEU* 1.3 75.7 - - - +
175B ALA* 1.3 68.7 + - - +
176B ILE 3.5 0.7 + - - -
187B PHE* 3.4 4.6 - - - -
188B GLU* 2.9 32.5 + - - +
190B LEU* 4.2 15.2 - - + +
379B GLN* 3.3 28.0 + - - +
380B GLY* 3.7 13.9 - - - +
381B PHE* 3.9 6.1 - - - -
384B SER* 2.8 31.1 + - - +
385B ARG 4.1 0.4 - - - -
386B PRO* 4.0 15.7 - - + +
501B C2E 3.1 40.7 + - - -
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B LEU 4.3 0.2 - - - -
174B GLN* 1.3 80.4 - - - +
176B ILE* 1.3 61.5 + - - +
177B VAL* 3.9 15.3 + - + +
184B VAL* 4.0 7.9 - - + -
186B SER 3.5 5.8 - - - -
187B PHE* 4.0 21.0 - - + -
378B PHE 4.1 3.5 - - - +
379B GLN* 4.2 8.1 - - - +
380B GLY 4.9 1.2 + - - -
383B PHE* 5.5 0.9 - - - +
384B SER* 3.5 21.2 + - - +
394B ILE* 3.9 22.4 - - + -
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Residues in contact with ILE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLN 3.5 2.4 + - - +
175B ALA* 1.3 71.4 - - - +
177B VAL* 1.3 56.0 + - - +
184B VAL* 3.6 1.9 - - - -
185B SER* 2.7 43.3 + - - +
186B SER* 2.7 38.8 + - - +
188B GLU* 4.9 5.8 - - + +
237B ALA* 5.2 1.8 - - + -
272B GLU* 4.8 3.1 - - - +
321B LYS* 3.9 13.7 - - - +
323B LYS* 3.9 18.4 - - - +
357B VAL* 3.8 23.1 - - + -
377B LEU* 4.6 3.1 - - + -
378B PHE 3.4 14.1 - - - +
379B GLN* 3.7 35.7 - - + +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ALA* 3.9 20.4 - - + +
176B ILE* 1.3 78.8 - - - +
178B GLU* 1.3 61.0 + - - +
179B PRO* 3.7 5.1 - - + +
183B ARG 3.6 4.5 - - - -
184B VAL* 4.5 4.5 - - + -
185B SER 4.7 0.2 - - - -
377B LEU* 3.5 8.0 - - - +
378B PHE* 2.7 46.0 + - + +
383B PHE* 3.6 43.1 - - + -
394B ILE* 3.8 26.5 - - + -
396B TRP* 3.9 14.1 - - + -
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B VAL* 1.3 72.3 - - - +
179B PRO* 1.3 65.8 - - - +
180B ALA* 3.2 8.5 + - + +
181B LYS* 3.4 35.2 + - - +
182B LYS 3.0 16.8 + - - -
183B ARG* 2.7 55.7 + - + +
185B SER* 5.2 0.7 - - - -
376B ARG* 3.6 24.3 - - + +
377B LEU* 3.7 15.4 - - + +
396B TRP* 4.0 2.0 - - - -
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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