Contacts of the strand formed by residues 216 - 221 (chain C) in PDB entry 4FJV
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 VAL 216 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 4.1 10.3 - - + +
59C SER* 3.6 19.3 - - - +
60C TYR* 3.5 42.0 - - + +
189C ILE* 4.1 6.7 - - + -
190C ALA 3.2 5.7 + - - +
191C LEU* 3.4 23.9 - - + -
192C GLN 2.8 25.6 + - - -
214C PRO* 3.7 4.7 - - - +
215C SER* 1.3 87.2 - - - +
217C TYR* 1.3 65.6 + - - +
218C LEU* 3.6 19.7 - - + -
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Residues in contact with TYR 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PHE* 3.4 38.1 - + + -
59C SER* 4.7 0.8 + - - -
192C GLN* 3.3 41.3 - - + +
194C GLU* 5.9 0.2 - - + -
214C PRO* 3.9 38.0 + - + +
215C SER 4.8 4.0 - - - -
216C VAL* 1.3 77.7 - - - +
218C LEU* 1.3 68.9 + - - +
227C ILE* 3.8 2.8 - - - +
228C LEU* 2.9 41.5 + - + +
229C TYR* 5.5 0.2 - - - -
230C ALA* 3.9 24.7 - - + +
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C PHE* 3.8 32.3 - - + +
55C ALA* 3.9 25.4 - - + +
56C LEU* 4.7 2.9 - - + +
191C LEU* 3.8 23.1 - - + -
192C GLN 2.9 8.8 + - - +
193C VAL* 3.6 5.4 - - + -
194C GLU* 2.9 26.3 + - - +
216C VAL* 3.6 13.7 - - + -
217C TYR* 1.3 83.8 - - - +
219C LEU* 1.3 60.4 + - - +
220C TYR 3.9 0.4 - - - -
225C TYR* 4.0 24.7 - - + -
226C ASN 3.2 13.2 - - - +
227C ILE* 4.0 9.4 - - + -
228C LEU* 3.7 8.1 - - - +
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE* 4.0 26.2 - - + -
32C ILE* 6.2 0.4 - - + -
35C LEU* 3.8 18.6 - - + -
42C ILE* 4.1 12.1 - - + -
194C GLU* 3.9 8.7 - - + +
196C VAL* 3.5 35.7 - - + -
218C LEU* 1.3 72.7 - - - +
220C TYR* 1.3 63.9 + - - +
221C LYS* 3.7 23.9 + - + +
224C HIS 3.1 6.4 - - - +
225C TYR* 3.4 1.5 - - - -
226C ASN* 2.8 41.0 + - + +
228C LEU* 3.7 18.3 - - + +
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Residues in contact with TYR 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C VAL* 3.6 16.6 - - + -
194C GLU 2.8 15.9 + - - +
195C TYR* 3.5 46.1 + + - -
196C VAL* 3.0 27.2 + - - +
218C LEU 3.9 0.8 + - - -
219C LEU* 1.3 71.8 - - - +
221C LYS* 1.3 59.6 + - - +
223C SER* 3.5 29.2 + - - -
224C HIS 3.3 9.2 - - - -
225C TYR* 3.5 32.1 - + + -
72D ARG 4.1 2.0 + - - -
73D LEU* 3.7 19.8 - - + -
74D ARG* 2.7 32.8 + - - +
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Residues in contact with LYS 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 5.1 10.5 - - - -
21C ASP* 4.9 8.5 + - - +
22C HIS* 2.9 38.5 + - + +
28C TYR* 4.2 11.7 - - + -
32C ILE* 5.2 4.3 - - + -
196C VAL* 3.7 33.7 - - + +
219C LEU* 3.7 29.1 + - + +
220C TYR* 1.3 78.6 - - - +
222C THR* 1.3 92.5 + - + +
223C SER 3.2 0.7 - - - +
224C HIS* 3.0 21.5 + - - +
226C ASN* 5.9 5.1 - - - +
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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