Contacts of the helix formed by residues 352 - 374 (chain C) in PDB entry 2GL7
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 SER 352 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353C GLN* 1.3 61.6 + - - +
354C GLU* 4.5 3.1 + - - +
355C GLN* 3.0 42.7 + - - +
356C LEU* 3.2 26.7 + - - +
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Residues in contact with GLN 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C SER* 1.3 73.5 - - - +
354C GLU* 1.3 66.2 + - - +
356C LEU* 3.2 20.4 + - - +
357C GLU* 3.4 13.3 + - - +
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Residues in contact with GLU 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C SER* 4.5 3.0 + - - +
353C GLN* 1.3 78.6 - - - +
355C GLN* 1.3 64.3 + - + +
357C GLU* 3.4 16.7 + - - +
358C HIS* 3.4 10.9 + - - +
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Residues in contact with GLN 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASP* 4.5 10.1 - - - +
352C SER* 3.0 29.8 + - - +
353C GLN 3.3 0.6 - - - -
354C GLU* 1.3 76.5 - - + +
356C LEU* 1.3 63.1 + - - +
357C GLU 3.4 0.2 - - - -
358C HIS* 3.5 15.5 + - + +
359C ARG* 3.2 20.6 + - - +
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Residues in contact with LEU 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C SER 3.2 18.5 + - - +
353C GLN* 3.2 20.2 + - - +
355C GLN* 1.3 74.7 - - - +
357C GLU* 1.3 63.3 + - - +
359C ARG* 3.4 9.4 + - - +
360C GLU* 3.2 22.2 + - - +
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Residues in contact with GLU 357 (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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353C GLN* 3.4 9.3 + - - +
354C GLU* 3.4 11.3 + - - +
355C GLN 3.4 0.2 - - - -
356C LEU* 1.3 75.8 - - - +
358C HIS* 1.3 65.1 + - - +
360C GLU* 3.4 5.1 + - - +
361C ARG* 3.1 26.4 + - - +
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Residues in contact with HIS 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 6.1 0.2 - - + -
162A ASP* 2.9 35.4 + - - -
163A GLU* 5.7 3.6 - - + +
164A ASP* 4.9 11.0 - - + -
167A VAL* 5.5 0.4 - - + -
354C GLU 3.4 9.6 + - - +
355C GLN* 3.5 18.4 - - + +
357C GLU* 1.3 79.9 - - - +
359C ARG* 1.3 55.5 + - - +
361C ARG* 4.1 4.1 - - - +
362C SER* 2.8 53.7 + - - -
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Residues in contact with ARG 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASP* 3.2 34.4 + - - +
166A VAL* 3.5 35.7 - - + +
167A VAL* 4.5 7.8 - - + +
355C GLN 3.2 12.6 + - - +
356C LEU* 3.7 10.9 - - - +
357C GLU 3.2 0.4 - - - -
358C HIS* 1.3 75.6 - - - +
360C GLU* 1.3 60.1 + - - +
362C SER* 3.2 4.9 + - - -
363C LEU* 2.8 47.3 + - + +
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Residues in contact with GLU 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C LEU 3.2 12.6 + - - +
357C GLU* 3.4 6.0 + - - +
359C ARG* 1.3 79.4 - - - +
361C ARG* 1.3 61.3 + - - +
363C LEU* 3.8 5.6 + - - +
364C GLN* 3.2 26.9 + - - +
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Residues in contact with ARG 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C GLU 3.1 17.1 + - - +
358C HIS* 4.1 4.7 - - - +
360C GLU* 1.3 74.1 - - - +
362C SER* 1.3 60.3 + - - +
364C GLN* 3.2 7.5 + - - +
365C THR* 2.9 31.8 + - - +
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Residues in contact with SER 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 3.8 17.9 - - - +
167A VAL* 3.6 23.7 - - - +
358C HIS* 2.8 43.9 + - - -
359C ARG 3.7 0.7 - - - -
361C ARG* 1.3 77.0 - - - +
363C LEU* 1.3 60.6 + - - +
365C THR* 3.3 10.2 + - - -
366C LEU* 3.2 28.7 + - - +
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Residues in contact with LEU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 4.0 22.2 - - + +
167A VAL* 5.5 4.0 - - + +
170A LYS* 4.6 22.0 - - + -
359C ARG* 2.8 37.7 + - + +
360C GLU* 4.2 4.9 - - - +
362C SER* 1.3 74.4 - - - +
364C GLN* 1.3 63.2 + - - +
366C LEU* 3.4 11.8 + - + +
367C ARG* 3.2 21.1 + - - +
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Residues in contact with GLN 364 (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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360C GLU 3.2 20.6 + - - +
361C ARG* 3.2 8.2 + - - +
363C LEU* 1.3 75.4 - - - +
365C THR* 1.3 64.6 + - - +
367C ARG* 3.3 12.5 + - - +
368C ASP* 3.1 25.5 + - - +
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Residues in contact with THR 365 (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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155A GLU* 3.3 37.7 - - + +
159A LEU* 4.2 12.7 - - + +
361C ARG* 2.9 18.3 + - - +
362C SER* 3.3 11.6 + - - -
364C GLN* 1.3 74.7 - - - +
366C LEU* 1.3 63.4 + - - +
368C ASP* 3.3 8.8 + - + +
369C ILE* 3.1 30.9 + - + +
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Residues in contact with LEU 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 4.0 22.9 - - + -
159A LEU* 3.9 27.8 - - + -
167A VAL* 4.3 20.2 - - + +
170A LYS* 4.4 16.2 - - + -
171A ALA* 4.1 10.1 - - - +
174A MET* 3.5 36.4 - - + +
362C SER 3.2 25.6 + - - +
363C LEU* 3.5 14.8 - - + +
364C GLN 3.2 0.6 - - - -
365C THR* 1.3 78.9 - - - +
367C ARG* 1.3 56.1 + - - +
369C ILE* 3.2 5.6 + - + +
370C GLN* 3.0 23.9 + - - +
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Residues in contact with ARG 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C LEU 3.2 10.5 + - - +
364C GLN* 3.3 18.8 + - - +
366C LEU* 1.3 78.3 - - - +
368C ASP* 1.3 61.4 + - - +
370C GLN* 3.5 12.2 + - - +
371C ARG* 3.3 21.1 + - - +
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Residues in contact with ASP 368 (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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364C GLN* 3.1 17.2 + - - +
365C THR* 3.4 13.0 - - + +
366C LEU 3.2 0.2 - - - -
367C ARG* 1.3 74.1 - - - +
369C ILE* 1.3 65.2 + - + +
371C ARG* 3.3 15.2 + - - +
372C MET* 3.5 28.8 + - + +
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Residues in contact with ILE 369 (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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152A ALA* 4.1 17.0 - - + +
155A GLU* 4.1 30.5 - - + -
156A LEU* 4.4 15.9 - - + -
159A LEU* 4.4 11.4 - - + -
174A MET* 4.0 11.2 - - - -
365C THR* 3.1 23.3 + - + +
366C LEU* 3.2 8.0 + - - +
368C ASP* 1.3 77.0 - - + +
370C GLN* 1.3 63.1 + - - +
372C MET* 3.2 16.2 + - + +
373C LEU* 3.1 45.3 + - + +
233D LYS* 5.7 5.8 - - - +
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Residues in contact with GLN 370 (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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174A MET* 4.0 23.5 - - + +
366C LEU 3.0 16.3 + - - +
367C ARG* 3.8 12.4 - - - +
368C ASP 3.3 0.2 - - - -
369C ILE* 1.3 76.0 - - - +
371C ARG* 1.3 57.3 + - - +
373C LEU* 4.8 0.2 - - - -
374C PHE* 3.0 58.4 + - + +
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Residues in contact with ARG 371 (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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367C ARG 3.3 11.3 + - - +
368C ASP* 3.6 11.7 - - - +
369C ILE 3.2 0.4 - - - -
370C GLN* 1.3 76.3 - - - +
372C MET* 1.3 65.2 + - + +
373C LEU 3.5 0.2 + - - -
374C PHE 3.5 17.6 - - - +
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Residues in contact with MET 372 (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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148A LEU* 3.6 31.7 - - + +
152A ALA* 6.6 0.2 - - - -
368C ASP* 3.5 25.9 + - + +
369C ILE* 3.2 17.8 + - - +
371C ARG* 1.3 81.2 - - + +
373C LEU* 1.3 65.8 + - + +
374C PHE 5.2 0.3 - - - +
233D LYS* 4.8 18.2 - - - +
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Residues in contact with LEU 373 (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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145A ASP* 5.6 1.9 - - - +
148A LEU* 3.7 38.4 - - + +
149A ALA* 4.5 1.3 - - + +
152A ALA* 3.9 13.2 - - + -
156A LEU* 4.7 0.7 - - + -
174A MET* 5.0 3.6 - - - -
178A LEU* 3.8 36.1 - - + -
369C ILE* 3.1 36.9 + - + +
372C MET* 1.3 86.4 - - + +
374C PHE* 1.3 87.0 + - + +
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Residues in contact with PHE 374 (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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174A MET* 4.5 15.3 - - + -
177A GLN* 4.0 36.1 - - + -
178A LEU* 4.3 10.1 - - + -
181A LYS* 3.7 36.1 - - + -
370C GLN* 3.0 47.2 + - + +
371C ARG* 3.5 18.1 - - - +
372C MET 5.0 0.4 - - - +
373C LEU* 1.3 102.3 - - + +
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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