Contacts of the helix formed by residues 345 - 354 (chain I) in PDB entry 6C6U
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 345 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225I PHE* 3.9 11.2 - - + -
296I VAL* 6.2 1.1 - - + -
338I THR* 3.8 32.1 - - + -
339I ASN 4.6 3.8 - - - +
343I HIS 4.2 0.2 - - - +
344I GLY* 1.3 81.7 - - - +
346I TYR* 1.3 59.7 + - + +
347I ILE 3.4 2.0 - - - -
348I SER* 3.2 16.3 + - - -
349I GLU* 2.8 44.8 + - + +
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Residues in contact with TYR 346 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I PHE* 3.8 23.3 - + + -
192I ASP* 3.4 48.2 + - + +
194I LEU* 5.2 5.2 - - + -
340I ASP 5.4 3.6 + - - -
344I GLY* 3.1 38.1 + - - -
345I PRO* 1.3 70.2 - - + +
347I ILE* 1.3 60.1 + - + +
349I GLU* 3.9 2.0 - - - +
350I THR* 2.5 39.0 + - - +
433I ILE* 4.5 21.1 - - + -
436I ARG* 3.5 45.9 + - + +
437I ASN* 4.1 11.9 + - - -
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Residues in contact with ILE 347 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I LEU* 3.9 19.7 - - + -
207I THR* 4.4 10.5 - - + -
220I ILE* 4.1 25.8 - - + -
221I LEU* 4.2 3.8 - - + -
224I PHE* 3.8 26.7 - - + +
225I PHE* 3.7 22.6 - - + -
345I PRO 3.4 0.2 - - - -
346I TYR* 1.3 74.6 - - - +
348I SER* 1.3 57.3 + - - +
350I THR* 3.4 3.9 + - - +
351I LEU* 2.9 37.2 + - + +
429I MET* 4.4 11.7 - - + -
433I ILE* 3.8 30.5 - - + -
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Residues in contact with SER 348 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221I LEU* 5.4 0.7 - - - -
225I PHE* 4.3 10.2 - - - -
296I VAL* 4.2 11.5 - - - +
314I ASN* 2.4 37.2 + - - +
336I LEU* 5.5 2.2 - - - -
338I THR* 5.7 1.1 - - - -
345I PRO* 3.2 23.9 + - - -
347I ILE* 1.3 77.4 - - - +
349I GLU* 1.3 61.1 + - - +
351I LEU 3.3 1.2 + - - -
352I ARG* 3.0 40.3 + - - +
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Residues in contact with GLU 349 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191I LYS 5.5 3.1 - - - +
192I ASP* 4.7 7.2 - - + +
193I ASN* 3.4 17.6 - - - +
345I PRO* 2.8 35.4 + - + +
346I TYR* 4.1 2.7 - - - +
348I SER* 1.3 73.3 + - - +
350I THR* 1.3 57.8 + - - +
352I ARG* 3.2 23.5 + - - +
353I VAL* 3.0 35.3 + - - +
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Residues in contact with THR 350 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I ASN* 4.1 4.8 - - + -
194I LEU* 3.2 47.4 + - + +
205I PRO* 4.0 6.6 - - + +
206I ALA 3.8 8.7 - - - +
207I THR* 3.5 26.9 - - + +
346I TYR 2.5 24.1 + - - -
347I ILE* 3.5 8.1 - - - -
348I SER 3.2 0.2 - - - -
349I GLU* 1.3 76.0 - - - +
351I LEU* 1.3 60.6 + - - +
353I VAL* 3.2 9.0 + - - +
354I ASP* 3.2 21.7 + - - +
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Residues in contact with LEU 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207I THR* 3.4 29.6 - - + +
211I ARG* 3.7 28.8 + - - +
217I THR* 3.8 21.5 - - + -
220I ILE* 4.3 14.8 - - + -
221I LEU* 4.3 5.6 - - + -
314I ASN* 3.4 30.1 - - + +
347I ILE* 2.9 28.1 + - + +
350I THR* 1.3 75.5 - - - +
352I ARG* 1.3 60.8 + - - +
354I ASP* 3.4 24.0 + - - +
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Residues in contact with ARG 352 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296I VAL* 4.2 11.7 - - - +
314I ASN* 3.0 35.8 + - - +
315I MET* 3.4 8.1 - - - +
316I GLU* 2.8 41.3 + - - +
348I SER* 3.0 26.0 + - - +
349I GLU* 3.2 27.8 + - - +
351I LEU* 1.3 79.4 - - - +
353I VAL* 1.3 61.2 + - + +
354I ASP 3.3 3.0 - - - +
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Residues in contact with VAL 353 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191I LYS* 6.0 2.7 - - - +
193I ASN* 4.1 24.9 - - - +
195I PHE* 5.1 8.5 - - + -
205I PRO* 4.1 20.0 - - + +
349I GLU* 3.0 19.1 + - + +
350I THR* 3.2 7.3 + - - +
352I ARG* 1.3 79.4 - - + +
354I ASP* 1.3 65.5 + - - +
355I PRO* 3.4 8.8 - - - +
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Residues in contact with ASP 354 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205I PRO* 3.3 29.3 - - - +
207I THR* 2.3 31.1 + - - -
208I ILE* 4.4 8.8 + - - +
211I ARG* 4.7 4.4 + - - +
350I THR 3.2 9.4 + - - +
351I LEU* 3.4 25.8 - - + +
352I ARG 3.3 4.5 - - - +
353I VAL* 1.3 77.2 - - - +
355I PRO* 1.3 65.8 - - + +
356I THR* 4.2 21.4 + - - +
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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
------------------------------------------------------------
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