Contacts of the helix formed by residues 420 - 430 (chain A) in PDB entry 5C51
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 HIS 420 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ASP* 3.4 15.4 + - - -
139A PHE* 5.0 2.0 - - + -
140A ARG* 3.2 46.8 + - + +
418A CYS 3.3 8.8 - - - +
419A PRO* 1.3 83.3 - - + +
421A PRO* 1.3 80.1 - - + +
422A VAL* 3.3 33.8 + - + +
423A THR* 3.5 14.9 + - - +
424A LEU* 4.0 2.8 + - - +
1075A LEU* 3.6 42.9 - - + +
1076A GLY 4.9 2.5 - - - +
1077A CYS* 4.9 2.7 - - - -
1111A LEU* 5.9 0.2 - - + -
1163A MET* 6.3 1.1 - - + -
1167A LYS* 4.1 7.6 + - - -
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Residues in contact with PRO 421 (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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140A ARG* 3.6 39.3 - - + +
143A ALA* 3.5 19.9 - - + +
144A GLN* 3.7 22.9 - - + +
147A SER* 4.7 3.6 - - - +
151A LEU* 6.3 1.6 - - + -
419A PRO 3.4 7.6 - - - +
420A HIS* 1.3 95.4 - - + +
422A VAL* 1.3 64.2 + - - +
423A THR 3.2 0.4 - - - -
424A LEU* 3.0 15.0 + - + +
425A ALA* 2.9 21.8 + - - +
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PHE* 3.9 23.1 - - + +
143A ALA* 3.6 8.5 - - + -
420A HIS* 3.2 29.4 - - + +
421A PRO* 1.3 79.5 - - - +
423A THR* 1.3 57.0 + - - +
426A GLY* 2.9 28.8 + - - -
1075A LEU* 4.3 13.0 - - + -
1107A ASP 4.8 0.4 - - - +
1110A HIS* 3.9 20.4 - - + +
1111A LEU* 3.7 38.1 - - + +
1114A VAL* 4.0 8.9 - - + +
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Residues in contact with THR 423 (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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414A PHE* 4.4 8.7 - - + -
418A CYS* 4.6 6.1 - - + -
420A HIS 3.5 8.3 + - - -
421A PRO 3.2 0.6 - - - -
422A VAL* 1.3 78.2 - - - +
424A LEU* 1.3 57.0 + - - +
426A GLY 3.8 0.2 - - - -
427A MET* 2.9 47.9 + - - +
852A ARG* 4.1 15.5 - - - +
1075A LEU* 3.4 12.1 - - - +
1077A CYS* 3.0 30.3 - - - -
1107A ASP* 3.6 5.0 + - - -
1110A HIS* 3.7 26.6 + - + -
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Residues in contact with LEU 424 (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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147A SER* 4.5 9.2 - - - +
150A TYR* 6.1 1.1 - - + -
151A LEU* 3.7 42.4 - - + -
292A LEU* 4.6 15.3 - - + -
411A LEU* 6.4 1.8 - - + -
414A PHE* 4.2 22.8 - - + -
415A LEU* 4.4 13.9 - - + -
418A CYS 6.0 0.4 - - - +
420A HIS 4.0 3.0 + - - +
421A PRO* 3.0 19.9 + - + +
423A THR* 1.3 76.0 - - - +
425A ALA* 1.3 60.5 + - - +
427A MET* 3.1 8.2 + - + +
428A LEU* 2.9 43.1 + - + +
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Residues in contact with ALA 425 (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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143A ALA* 3.8 19.7 - - - +
146A GLN* 4.1 15.3 - - + +
147A SER* 4.2 5.8 - - - -
421A PRO 2.9 15.3 + - - +
424A LEU* 1.3 73.8 - - - +
426A GLY* 1.3 57.6 + - - +
428A LEU* 3.0 14.4 + - - +
429A GLU* 2.9 31.4 + - - +
1114A VAL* 3.6 20.9 - - + -
1117A LYS* 5.7 3.1 + - + +
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Residues in contact with GLY 426 (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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422A VAL 2.9 19.3 + - - -
423A THR 3.8 0.9 - - - -
425A ALA* 1.3 77.9 - - - +
427A MET* 1.3 55.2 + - - +
429A GLU 3.6 0.2 + - - -
430A MET* 3.1 30.5 + - - +
1110A HIS* 4.1 24.7 - - - -
1113A LEU* 3.4 11.4 - - - +
1114A VAL* 3.8 9.1 - - - +
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Residues in contact with MET 427 (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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291A PHE 4.7 4.4 - - - +
292A LEU* 5.3 15.9 - - + -
293A ASP 5.2 1.8 - - - +
296A SER* 3.5 31.4 - - - +
297A MET* 4.8 3.4 - - + +
300A ALA* 5.3 2.0 - - - -
414A PHE* 3.5 38.8 - - + -
423A THR* 2.9 26.6 + - - +
424A LEU* 3.4 6.3 - - + +
426A GLY* 1.3 76.3 - - - +
428A LEU* 1.3 64.2 + - + +
430A MET* 3.7 7.6 + - + -
431A GLY* 3.7 4.2 + - - -
846A THR* 3.2 36.5 + - + +
847A ALA* 4.4 11.9 - - + -
852A ARG* 5.4 2.5 - - + -
1110A HIS* 4.4 14.6 - - + +
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Residues in contact with LEU 428 (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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146A GLN 4.6 1.3 - - - +
147A SER* 3.7 23.1 - - - -
150A TYR* 3.6 35.4 - - + -
265A LEU* 4.7 7.2 - - + -
290A ARG* 3.9 33.4 + - + +
291A PHE 3.6 24.2 + - - +
292A LEU* 3.7 19.7 - - + -
424A LEU* 2.9 22.9 + - + +
425A ALA* 3.0 10.3 + - + +
427A MET* 1.3 80.9 - - - +
429A GLU* 1.3 60.6 + - - +
430A MET 3.5 0.3 + - - -
431A GLY* 3.6 6.6 + - - -
432A VAL* 3.8 11.6 + - - +
1117A LYS* 5.8 2.0 - - - +
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Residues in contact with GLU 429 (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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290A ARG* 3.6 14.5 - - - +
425A ALA 2.9 12.6 + - - +
426A GLY 4.4 2.2 - - - +
428A LEU* 1.3 73.8 - - - +
430A MET* 1.3 60.0 + - - +
431A GLY 3.1 5.2 - - - -
432A VAL* 3.2 18.8 + - + +
433A SER* 5.5 0.3 - - - -
1113A LEU* 3.0 39.7 - - + +
1114A VAL* 4.0 1.2 + - - +
1117A LYS* 3.8 20.8 - - + +
1128A ARG* 3.0 32.0 + - - +
1130A CYS* 4.3 16.6 - - + +
1139A TYR* 3.4 26.8 + - - -
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Residues in contact with MET 430 (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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426A GLY 3.1 14.3 + - - +
427A MET* 4.1 7.4 - - + +
428A LEU 3.3 0.6 - - - -
429A GLU* 1.3 76.6 - - - +
431A GLY* 1.3 58.4 + - - +
432A VAL 3.5 0.4 - - - -
433A SER* 4.7 5.7 + - - -
844A VAL* 3.9 17.9 - - + +
846A THR* 3.2 37.8 - - + +
852A ARG 4.3 7.6 - - - +
853A ARG* 6.0 0.4 - - - -
854A ALA* 5.5 14.8 - - + +
1106A VAL* 5.5 0.7 - - + -
1109A LEU* 4.2 19.7 - - - -
1110A HIS* 3.4 32.1 - - + +
1113A LEU* 3.8 21.3 - - + +
1130A CYS* 5.7 2.7 - - - -
1132A SER* 4.2 14.3 + - - +
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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