Contacts of the helix formed by residues 291 - 300 (chain C) in PDB entry 6TXA
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 PRO 291 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285C TRP* 3.6 10.2 - - + +
290C ARG* 1.3 101.9 - - + +
292C GLU* 1.3 65.6 + - - +
293C ASN* 3.2 30.5 - - - +
294C LYS* 3.1 24.2 + - + +
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Residues in contact with GLU 292 (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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284C LEU* 5.6 4.0 - - - +
285C TRP* 3.4 53.6 + - + +
291C PRO* 1.3 73.7 - - - +
293C ASN* 1.3 57.4 + - - +
294C LYS 3.1 5.0 + - - -
295C SER* 3.2 18.9 + - - -
345C ASN* 3.4 23.9 - - - +
346C GLU* 4.2 6.2 - - + +
347C LEU 3.8 10.7 + - - -
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Residues in contact with ASN 293 (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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189C LEU 5.0 3.3 - - - +
291C PRO* 3.4 25.1 - - - +
292C GLU* 1.3 77.4 - - - +
294C LYS* 1.3 73.9 + - - +
295C SER 3.7 0.7 - - - -
296C PHE* 3.7 5.5 - - - -
347C LEU* 3.4 33.8 - - + +
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Residues in contact with LYS 294 (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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189C LEU 4.0 8.3 - - - +
190C GLN* 3.2 27.6 + - - +
191C ILE* 4.7 1.3 - - - +
192C SER* 4.6 4.2 + - - -
195C ASP* 2.8 31.4 + - - +
290C ARG* 4.3 18.3 - - + +
291C PRO* 3.1 15.6 + - + +
292C GLU 3.1 0.6 - - - -
293C ASN* 1.3 96.5 + - - +
295C SER* 1.3 61.8 + - - +
296C PHE* 3.2 19.7 - - + -
297C LEU* 3.2 33.0 + - + +
298C TYR* 4.2 7.3 - - - -
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Residues in contact with SER 295 (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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285C TRP* 3.2 34.1 - - - -
291C PRO 3.7 1.0 + - - -
292C GLU 3.2 10.3 + - - -
293C ASN 3.7 0.4 - - - -
294C LYS* 1.3 77.3 - - - +
296C PHE* 1.3 62.5 + - - +
298C TYR* 3.0 23.6 + - - +
299C GLU* 3.9 7.1 + - - +
305C ARG* 5.1 3.1 + - - -
346C GLU* 3.2 26.5 + - - +
347C LEU 2.6 25.0 + - - -
348C ARG* 4.1 3.8 - - - +
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Residues in contact with PHE 296 (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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182C LEU* 4.4 9.6 - - + -
189C LEU* 3.9 25.8 - - + -
191C ILE* 3.6 33.7 - - + -
293C ASN 3.7 19.3 - - - -
294C LYS* 3.9 14.4 - - + -
295C SER* 1.3 77.2 - - - +
297C LEU* 1.3 100.1 + - + +
299C GLU* 3.1 27.1 + - - +
300C ILE* 4.0 2.8 - - + +
340C VAL* 3.7 23.1 - - + -
347C LEU* 3.0 24.0 + - + +
349C ILE* 3.7 28.9 - - + +
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Residues in contact with LEU 297 (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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179C VAL* 3.5 29.2 - - + -
191C ILE* 4.8 3.4 - - + -
195C ASP* 3.9 30.3 - - + +
199C VAL* 4.2 7.2 - - + -
267C PHE* 3.7 30.7 - - + -
271C GLN* 3.4 18.7 + - - +
290C ARG* 4.6 1.8 - - + +
294C LYS* 3.5 27.6 - - + +
295C SER 3.1 1.0 - - - -
296C PHE* 1.3 106.5 - - + +
298C TYR* 1.3 60.5 + - - +
299C GLU 3.4 0.5 + - - -
300C ILE* 3.5 18.4 + - + +
301C VAL 4.8 0.3 + - - -
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Residues in contact with TYR 298 (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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267C PHE* 3.4 22.1 - + - -
270C GLU* 2.7 35.8 + - + -
271C GLN* 4.1 23.4 - - + +
285C TRP* 3.9 11.9 - + - -
287C TYR* 3.4 57.5 - + + +
290C ARG* 3.1 31.9 + - + -
294C LYS 4.2 2.9 - - - -
295C SER* 3.0 24.5 + - - +
297C LEU* 1.3 77.4 - - - +
299C GLU* 1.3 59.8 + - + +
300C ILE 3.4 1.2 + - - -
301C VAL 5.1 0.4 - - - -
302C SER 3.3 23.2 + - - +
303C ASN* 4.3 0.7 - - - -
304C LYS* 5.0 1.7 + - - +
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Residues in contact with GLU 299 (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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178C LEU* 5.3 1.6 - - - +
295C SER* 4.2 7.2 - - - +
296C PHE* 3.1 14.2 + - - +
298C TYR* 1.3 79.5 - - + +
300C ILE* 1.3 60.0 + - - +
303C ASN* 3.6 42.7 + - - +
304C LYS 6.0 0.4 - - - +
305C ARG* 3.1 37.2 + - + +
306C ASN* 5.4 2.1 + - - -
308C ILE 3.6 10.4 - - - +
309C ASP* 4.5 0.2 - - - -
348C ARG* 3.6 14.8 - - - +
349C ILE* 2.7 50.9 + - + +
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Residues in contact with ILE 300 (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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175C ALA* 3.7 32.5 - - + +
178C LEU* 3.9 26.2 - - + +
179C VAL* 3.7 38.1 - - + +
182C LEU* 4.7 6.5 - - + -
199C VAL* 3.9 14.4 - - + -
296C PHE 4.0 8.5 - - - +
297C LEU* 3.5 24.4 + - + +
298C TYR 3.4 2.0 - - - -
299C GLU* 1.3 79.2 - - - +
301C VAL* 1.3 63.7 + - + +
309C ASP* 3.4 4.4 - - - +
310C VAL* 3.0 29.4 + - + +
349C ILE* 4.1 4.7 - - + -
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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