Contacts of the helix formed by residues 368 - 380 (chain A) in PDB entry 1GXD
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 LEU 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LEU* 4.4 12.8 - - + -
111A VAL* 3.8 30.3 - - + -
114A ALA* 4.2 17.7 - - + -
115A PHE* 3.9 23.8 - - + -
144A PHE* 3.9 16.6 - - + -
178A PHE* 4.0 23.3 - - + -
184A TRP* 3.6 30.5 - - + -
185A THR 3.0 12.4 + - - +
186A LEU* 5.4 0.7 - - + -
366A TYR 3.2 3.2 + - - -
367A SER* 1.3 67.3 - - - +
369A PHE* 1.3 72.1 + - - +
371A VAL* 4.6 0.7 - - - +
372A ALA* 2.9 24.8 + - - +
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Residues in contact with PHE 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ALA* 3.8 15.1 - - + +
117A ARG* 3.0 76.3 - - + +
118A ALA* 3.8 7.5 - - - +
121A VAL* 4.0 18.8 - - + -
185A THR 4.8 0.2 + - - -
186A LEU* 4.9 5.6 - - + +
367A SER* 3.0 8.2 + - - +
368A LEU* 1.3 84.7 - - - +
370A LEU* 1.3 84.8 + - + +
372A ALA* 3.7 2.4 - - - +
373A ALA* 3.1 17.6 + - + +
402A PHE* 3.8 26.9 - + + -
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Residues in contact with LEU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A SER* 2.8 22.8 + - - +
369A PHE* 1.3 86.4 - - + +
371A VAL* 1.3 62.4 + - - +
373A ALA* 2.8 26.5 + - + +
374A HIS* 3.2 8.7 + - - +
391A LEU* 4.3 8.8 - - + +
396A TYR* 4.4 11.0 - - + -
397A THR 3.9 12.3 - - - +
398A TYR* 3.9 19.3 - - + -
399A THR* 3.9 28.9 - - + +
402A PHE* 3.7 42.2 - - + -
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Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 3.8 26.9 - - + -
163A ALA* 4.0 21.8 - - + -
178A PHE* 4.0 4.5 - - + -
184A TRP* 3.7 37.0 - - + -
366A TYR* 4.3 1.6 - - + -
367A SER 2.8 22.1 + - - +
368A LEU 4.4 0.9 - - - +
370A LEU* 1.3 71.0 - - - +
372A ALA* 1.3 62.3 + - - +
374A HIS* 3.7 7.0 + - + +
375A ALA* 3.1 20.6 + - - +
396A TYR* 4.0 18.4 - - + -
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Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE* 3.8 16.8 - - + -
118A ALA* 3.8 13.7 - - + -
178A PHE* 3.5 30.4 - - + -
368A LEU 2.9 20.0 + - - +
369A PHE 3.7 2.5 - - - +
371A VAL* 1.3 75.5 - - - +
373A ALA* 1.3 56.4 + - - +
375A ALA* 3.9 0.7 - - - -
376A PHE* 2.7 42.6 + - + -
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ALA* 3.7 16.1 - - + +
121A VAL* 4.8 11.0 - - + -
122A TRP* 3.3 12.3 + - - +
369A PHE* 3.1 13.7 + - + +
370A LEU* 2.8 16.4 + - + +
372A ALA* 1.3 79.3 - - - +
374A HIS* 1.3 67.7 + - - +
376A PHE* 2.9 6.9 + - - +
377A GLY 3.1 8.1 + - - -
391A LEU* 3.6 26.0 - - + -
402A PHE* 4.9 3.6 - - + -
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Residues in contact with HIS 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A CYS* 2.7 18.1 - - + -
370A LEU 3.2 6.2 + - - +
371A VAL* 3.9 10.5 - - + +
373A ALA* 1.3 75.1 - - - +
375A ALA* 1.3 69.9 + - + +
377A GLY 2.9 12.8 + - - -
378A HIS* 2.5 18.7 + + - -
384A HIS* 3.1 18.4 - + - -
391A LEU* 3.4 22.8 + - + +
392A MET* 3.3 24.3 - - + +
393A ALA 3.4 23.4 + - - -
394A PRO 4.6 0.4 + - - -
1634A ZN 1.8 37.6 - - - -
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Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ALA* 5.4 7.9 - - + -
164A HIS* 5.4 3.1 - - - +
165A ALA* 3.9 11.8 - - + +
176A SER* 4.5 12.1 - - - +
178A PHE* 4.5 10.8 - - + -
371A VAL* 3.1 16.1 + - + +
372A ALA* 3.4 10.3 - - - +
374A HIS* 1.3 87.1 - - + +
376A PHE* 1.3 65.5 + - + +
378A HIS* 2.8 28.4 + - - +
379A ALA 3.1 3.3 + - - -
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Residues in contact with PHE 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE* 3.9 15.0 - + - -
118A ALA* 3.4 28.7 - - + -
119A PHE* 3.6 50.3 - + + -
122A TRP* 3.7 15.5 - - + +
140A ILE* 4.4 6.1 - - + -
142A ILE* 3.4 31.9 - - + -
176A SER* 3.6 26.5 - - - -
178A PHE* 4.7 2.9 - + - -
372A ALA* 2.7 29.6 + - + +
373A ALA 3.5 4.0 - - - +
375A ALA* 1.3 72.7 - - - +
377A GLY* 1.3 63.6 + - - +
379A ALA* 2.9 5.6 + - + +
380A MET* 2.9 27.2 + - + +
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Residues in contact with GLY 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TRP* 3.2 28.0 - - - +
373A ALA 3.1 6.3 + - - -
374A HIS 2.9 9.0 + - - -
376A PHE* 1.3 73.2 - - - +
378A HIS* 1.3 56.4 + - - +
380A MET* 2.6 29.4 + - - +
381A GLY 3.0 0.3 + - - -
382A LEU* 3.0 24.9 + - - +
392A MET* 4.1 3.8 - - - -
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Residues in contact with HIS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A CYS* 3.8 0.2 - - - -
75A ASN* 3.0 28.5 + - + +
76A PRO 5.4 0.2 - - - -
165A ALA* 4.0 16.5 + - + +
166A PHE 4.4 2.5 - - - -
167A ALA* 3.6 13.2 + - - +
374A HIS* 2.5 31.2 + + - -
375A ALA* 2.8 14.1 + - - +
377A GLY* 1.3 72.3 - - - +
379A ALA* 1.3 55.7 + - - +
381A GLY* 2.9 22.2 + - - -
382A LEU 3.4 17.2 + - - +
383A GLU* 4.7 5.5 + - - -
384A HIS* 3.2 23.5 + + - -
392A MET* 3.8 9.6 - - + +
1634A ZN 1.8 38.8 - - - -
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A TRP* 2.7 24.4 + - - -
140A ILE* 4.6 9.0 - - + -
165A ALA* 4.6 1.6 - - + -
166A PHE 3.7 11.9 + - - +
168A PRO* 3.1 9.3 - - - +
174A GLY* 3.4 28.0 - - - +
176A SER* 4.4 6.5 - - - +
375A ALA 3.1 3.7 + - - +
376A PHE* 2.9 17.1 + - - +
378A HIS* 1.3 76.0 - - - +
380A MET* 1.3 62.3 + - + +
381A GLY 3.1 5.4 - - - -
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Residues in contact with MET 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PRO 4.1 2.9 - - - +
90A TRP* 3.4 24.0 - - + +
95A ILE* 4.1 0.7 - - - -
119A PHE* 4.4 6.3 - - + -
122A TRP* 4.6 5.8 - - + -
128A LEU* 3.7 26.5 - - + -
130A PHE* 3.4 38.1 - - + -
140A ILE* 4.5 2.9 - - + -
168A PRO* 3.6 5.2 - - - +
376A PHE* 2.9 40.5 + - + +
377A GLY* 2.6 17.1 + - - +
379A ALA* 1.3 79.2 - - + +
381A GLY* 1.3 56.8 + - - +
382A LEU 3.5 1.3 + - - -
412A ILE* 3.8 18.6 - - + -
415A LEU* 4.1 2.3 - - - +
416A TYR* 2.7 32.6 + - + -
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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