Contacts of the strand formed by residues 214 - 222 (chain A) in PDB entry 6VSU
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 ALA 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A PRO* 4.2 4.0 - - - +
179A VAL 2.9 10.5 - - - +
181A ILE* 3.5 30.5 - - + -
208A ILE* 4.4 3.8 + - + +
209A MET* 3.9 30.9 - - - +
212A GLY* 4.4 7.3 - - - -
213A TYR* 1.3 81.7 - - - +
215A ARG* 1.3 64.4 + - - +
216A ARG 3.9 7.6 - - - +
217A LEU* 5.0 0.7 - - + -
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Residues in contact with ARG 215 (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 PRO* 4.0 11.2 - - + +
179A VAL 2.8 10.4 + - - +
180A ASP* 2.7 37.8 + - - +
209A MET* 4.3 8.1 - - - +
214A ALA* 1.3 74.8 - - - +
216A ARG* 1.3 77.6 + - + +
217A LEU 4.0 1.0 + - - -
236A PHE 5.4 1.4 - - - +
237A GLY 5.6 1.6 - - - +
258A LEU* 5.3 0.4 - - - +
259A GLY 3.8 0.8 - - - +
260A GLU* 2.9 39.0 + - - +
261A GLY* 4.1 2.8 - - - -
262A VAL* 3.2 39.4 - - + +
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Residues in contact with ARG 216 (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 VAL 3.8 2.6 - - - +
180A ASP* 2.9 28.0 + - + +
181A ILE* 2.9 28.8 + - - -
214A ALA* 3.9 4.4 - - - +
215A ARG* 1.3 95.9 - - + +
217A LEU* 1.3 55.6 + - - +
218A LEU* 4.1 18.9 - - + +
237A GLY 5.8 2.2 - - - -
239A GLU* 3.0 41.0 + - - +
252A MET* 5.0 10.3 - - - +
256A LEU* 5.9 0.8 - - - +
257A LYS 3.7 10.1 + - - -
258A LEU* 3.5 21.9 - - - +
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Residues in contact with LEU 217 (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 ILE* 3.3 25.4 - - + +
183A HIS* 3.6 30.1 - - + -
190A ILE* 4.7 0.9 - - + -
205A PHE* 3.9 20.4 - - + -
209A MET* 3.9 29.6 - - + +
214A ALA* 5.0 0.4 - - + -
215A ARG 4.0 1.2 + - - -
216A ARG* 1.3 72.7 - - - +
218A LEU* 1.3 60.7 - - - +
219A GLN* 3.8 16.2 - - + +
237A GLY 5.3 4.0 + - - -
238A VAL* 3.5 35.6 - - + +
239A GLU* 2.9 29.0 + - - +
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Residues in contact with LEU 218 (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 ILE 2.8 14.6 + - - +
182A LEU* 4.0 12.5 - - + +
183A HIS* 2.7 34.9 + - - +
216A ARG* 4.1 27.4 - - + +
217A LEU* 1.3 75.9 - - - +
219A GLN* 1.3 58.0 + - - +
220A VAL* 4.0 5.7 + - + -
239A GLU* 3.4 37.2 - - + +
241A TYR* 4.2 15.9 - - + +
252A MET* 5.3 0.7 - - + -
253A LEU* 5.3 1.6 - - + -
256A LEU* 3.9 34.5 - - + -
258A LEU* 4.2 17.7 - - + -
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Residues in contact with GLN 219 (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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183A HIS* 2.8 29.0 + - - +
188A PRO* 2.8 36.4 + - - +
190A ILE* 4.7 3.1 - - - +
205A PHE* 4.3 2.2 - - - +
217A LEU* 3.8 15.5 - - + +
218A LEU* 1.3 71.2 - - - +
220A VAL* 1.3 60.5 + - - +
222A ILE* 3.8 19.5 - - + +
238A VAL* 3.5 20.6 - - + +
239A GLU 2.9 8.4 + - - +
240A GLN* 2.8 36.0 + - - +
241A TYR* 2.7 35.2 + - - +
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Residues in contact with VAL 220 (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 LEU* 3.8 22.7 - - + -
183A HIS 2.9 5.4 + - - +
184A LEU* 3.3 30.7 - - + +
185A ASP 2.9 25.9 + - - +
218A LEU* 4.2 7.0 - - + -
219A GLN* 1.3 79.5 - - - +
221A GLY* 1.3 62.3 + - - +
222A ILE* 3.5 1.3 - - - +
241A TYR* 4.0 8.1 - - + -
246A PHE* 5.3 0.7 - - + -
253A LEU* 3.7 37.5 - - + -
256A LEU* 5.4 0.2 - - + -
273A CYS* 4.5 0.9 - - - +
290A LEU* 4.6 6.1 - - + -
298A ILE* 4.0 19.7 - - + -
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Residues in contact with GLY 221 (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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185A ASP 3.1 10.8 - - - +
186A ALA* 3.5 0.3 - - - -
220A VAL* 1.3 74.5 - - - +
222A ILE* 1.3 64.8 + - - +
223A ARG* 3.0 27.9 + - - -
241A TYR* 3.5 4.8 + - - +
243A MET* 3.6 27.3 - - - +
246A PHE* 6.3 0.2 - - - -
273A CYS 4.8 0.4 - - - -
290A LEU* 4.0 12.8 - - - -
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Residues in contact with ILE 222 (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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185A ASP* 3.3 18.2 - - + +
186A ALA 3.3 5.6 - - - +
187A HIS 3.3 28.3 - - - +
188A PRO* 3.6 11.0 - - + -
219A GLN* 3.8 30.5 - - + +
221A GLY* 1.3 75.6 - - - +
223A ARG* 1.3 60.5 + - - +
224A SER 4.3 0.2 - - - +
225A ILE* 3.9 40.4 - - + -
240A GLN* 5.2 4.0 - - + -
241A TYR 3.2 18.0 + - - +
242A GLU* 3.2 14.1 - - + +
243A MET 2.8 30.8 + - - -
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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