Contacts of the strand formed by residues 197 - 204 (chain C) in PDB entry 5DFV
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 TRP 197 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A THR* 3.2 38.1 - - + -
168A SER* 3.8 14.3 + - - +
171A LYS* 3.8 23.7 - - + +
172A ASN* 5.7 1.7 - - - +
182A ILE* 5.0 1.3 - - + -
156C SER 5.3 0.9 - - - -
196C SER* 1.3 77.5 - - - +
198C MET* 1.3 63.2 + - - +
199C ASN* 4.3 0.9 - - - +
251C ARG* 3.1 40.3 - - - +
252C ILE* 3.2 35.0 - - - -
253C TYR* 3.3 42.0 - + + -
290C ASP 4.0 6.5 - - - -
292C ILE* 4.3 5.8 - - + -
332C ARG* 3.4 8.8 - - - +
351C GLU* 3.3 44.3 + - + +
352C GLY 5.3 1.9 + - - -
353C LYS 6.0 0.4 - - - -
355C GLY* 4.0 19.0 - - - -
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Residues in contact with MET 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU* 3.5 19.5 - - + -
122C CYS* 4.4 2.7 - - - -
124C ALA* 4.4 4.3 - - + -
152C TYR* 3.1 28.0 - - - +
154C PHE* 4.1 16.8 - - + -
196C SER* 6.3 0.4 - - - -
197C TRP* 1.3 75.9 - - - +
199C ASN* 1.3 66.0 + - - +
201C TRP* 4.2 7.2 - - - +
251C ARG* 3.2 2.3 - - - -
252C ILE* 3.0 46.5 + - + +
254C SER* 4.7 7.0 - - - +
313C ALA* 3.6 23.3 - - + +
330C CYS* 3.3 27.6 - - - -
331C ALA 3.6 14.8 - - - -
332C ARG* 3.9 3.1 - - + -
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Residues in contact with ASN 199 (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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197C TRP 4.3 0.4 - - - -
198C MET* 1.3 82.1 - - - +
201C TRP* 1.3 70.8 + - - +
202C VAL* 5.1 1.8 - - + -
212C TRP* 3.3 19.1 + - + +
214C GLY 3.4 7.0 - - - +
251C ARG* 3.3 17.9 - - - +
330C CYS* 3.7 2.4 - - - -
331C ALA* 2.6 45.3 + - + +
351C GLU* 3.1 37.1 + - - +
397C LEU* 3.5 24.1 - - + +
798D PHE* 4.1 4.0 - - - -
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Residues in contact with TRP 201 (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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106C GLN* 4.0 9.0 - - - -
120C ILE* 3.6 32.5 - - + -
121C SER 3.9 4.3 - - - -
122C CYS* 3.9 22.7 - - + -
198C MET* 4.2 17.6 + - + +
199C ASN* 1.3 81.2 + - - +
202C VAL* 1.3 67.3 + - - +
212C TRP* 4.0 1.2 - - - -
213C ILE* 2.9 36.9 + - + +
214C GLY 3.2 8.7 + - - +
252C ILE* 5.0 2.8 - - - +
304C LEU* 4.1 23.8 - - + +
313C ALA* 3.9 16.9 - - + +
314C TYR 3.8 26.2 + - - -
315C MET* 3.8 37.7 - - + -
328C TYR* 4.8 6.1 - - + -
329C PHE 3.0 28.5 - - - -
330C CYS* 4.3 2.5 - - + -
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Residues in contact with VAL 202 (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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199C ASN* 5.1 3.1 - - + -
201C TRP* 1.3 82.8 - - - +
203C LYS* 1.3 67.9 + - - +
210C LEU* 4.0 24.2 - - + -
211C GLU 3.2 20.9 - - - +
212C TRP* 4.5 11.9 - - + -
213C ILE* 4.3 3.3 - - - +
327C VAL 3.7 1.2 - - - +
328C TYR* 3.5 1.8 - - - +
329C PHE* 2.8 39.9 + - + +
331C ALA* 5.5 2.2 - - + -
397C LEU* 4.5 12.1 - - + -
401C TRP* 4.0 31.4 - - + -
801D PHE* 4.4 6.7 - - + -
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Residues in contact with LYS 203 (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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202C VAL* 1.3 73.9 - - - +
204C GLN* 1.3 66.5 + - - +
205C ARG* 3.7 23.9 - - + +
210C LEU* 3.8 1.6 - - - -
211C GLU* 2.8 61.1 + - + +
213C ILE* 3.9 11.0 - - + +
297C PHE* 4.0 14.6 - - + -
323C GLU 2.9 27.5 + - - -
324C ASP* 3.8 10.3 + - - +
326C ALA* 3.9 9.0 - - + -
327C VAL 3.9 2.7 - - - -
328C TYR* 3.4 43.2 + - + +
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Residues in contact with GLN 204 (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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203C LYS* 1.3 76.8 - - - +
205C ARG* 1.3 64.2 + - - +
206C PRO* 3.5 3.9 - - + +
208C LYS 3.9 11.3 + - - +
209C GLY 3.5 12.1 - - - +
210C LEU* 3.5 22.4 - - + +
326C ALA* 3.7 2.9 - - - -
327C VAL* 3.0 39.0 + - + +
329C PHE* 3.3 15.3 - - + -
604D GLN* 3.0 41.5 + - - -
733D TYR* 3.8 14.1 + - - -
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Residues in contact with ARG 205 (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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203C LYS* 3.7 21.5 - - + +
204C GLN* 1.3 73.5 - - - +
206C PRO* 1.4 77.9 + - + +
207C GLY 3.2 0.5 + - - -
208C LYS* 3.0 62.8 + - + +
209C GLY 4.3 3.0 + - - -
211C GLU* 5.9 0.4 - - - +
322C SER 3.5 6.7 + - - -
323C GLU* 3.3 51.1 + - - +
325C SER* 3.3 21.3 + - - -
326C ALA* 3.7 3.1 - - + -
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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