Contacts of the helix formed by residues 494 - 505 (chain A) in PDB entry 2B63
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 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A TYR* 3.9 0.2 - - - -
493A GLN* 1.3 80.9 + - - +
495A GLU* 1.3 58.3 + - - +
496A GLU* 3.9 14.4 - - - -
497A THR* 2.5 41.8 + - - -
498A ARG* 3.0 13.4 + - - +
1149B GLU* 3.1 10.7 + - - +
1153B GLU* 6.1 0.9 - - - +
99F LEU* 5.2 2.9 - - - -
64G THR* 4.4 20.0 + - - +
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Residues in contact with GLU 495 (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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376A TYR* 3.2 27.1 + - - +
378A GLU* 5.7 1.6 - - - +
494A SER* 1.3 70.1 - - - +
496A GLU* 1.3 60.3 + - - +
498A ARG* 3.5 22.8 + - - +
499A ALA* 3.4 18.2 + - - +
95F GLY* 4.8 2.0 - - - -
98F ALA* 3.9 23.6 - - + +
99F LEU* 3.9 22.0 - - + +
102F SER* 4.0 15.5 - - - +
116F ASP* 4.9 1.4 - - - +
117F PRO* 3.8 22.7 - - + +
118F LEU* 4.4 14.7 - - - +
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Residues in contact with GLU 496 (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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494A SER* 2.7 14.9 + - - -
495A GLU* 1.3 75.4 - - - +
497A THR* 1.3 71.7 + - - +
499A ALA* 3.4 5.5 - - - +
500A GLU* 3.3 17.3 + - - +
1145B SER* 4.2 20.0 + - - -
92F ARG* 5.6 4.9 + - - +
95F GLY* 3.9 27.8 - - - +
96F THR* 4.0 16.1 + - - +
99F LEU* 3.9 25.8 - - + +
63G PRO* 2.5 32.5 - - - +
64G THR* 3.6 8.0 - - - +
65G ASP 5.6 0.2 - - - +
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Residues in contact with THR 497 (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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492A PRO* 3.7 18.2 - - + -
494A SER* 2.5 22.3 + - - -
496A GLU* 1.3 78.9 - - - +
498A ARG* 1.3 67.5 + - - +
500A GLU* 2.6 26.5 + - - +
501A LEU* 3.3 4.2 + - + +
1145B SER* 4.5 4.4 + - - -
1146B PHE* 3.7 34.6 + - + +
1149B GLU* 3.0 38.7 + - - +
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Residues in contact with ARG 498 (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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376A TYR* 3.1 42.6 + - + +
378A GLU* 5.9 1.2 + - - -
434A ARG* 4.2 4.2 - - - +
439A ASN 4.8 0.2 + - - -
440A ASP* 3.0 35.2 + - - +
441A PRO* 3.2 41.9 + - + +
492A PRO* 4.3 18.8 - - + +
494A SER 3.2 15.0 - - - +
495A GLU* 3.5 26.4 + - - +
497A THR* 1.3 77.1 - - - +
499A ALA* 1.3 56.6 + - - +
501A LEU* 2.4 34.4 + - - +
502A SER* 2.9 12.8 + - - +
116F ASP* 5.4 5.5 + - - -
118F LEU* 6.2 2.0 - - + -
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Residues in contact with ALA 499 (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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495A GLU 3.4 7.6 + - - +
496A GLU 3.4 11.2 + - - +
498A ARG* 1.3 78.4 - - - +
500A GLU* 1.3 54.5 + - - +
502A SER* 3.2 10.5 - - - -
503A GLN* 2.7 42.9 + - + +
91F ALA 4.2 8.5 - - - +
94F LEU* 5.2 1.3 - - + -
95F GLY* 3.7 27.6 - - - +
118F LEU* 4.7 17.6 - - + +
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Residues in contact with GLU 500 (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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496A GLU 3.3 6.2 + - - +
497A THR* 2.6 21.2 + - - +
499A ALA* 1.3 75.5 - - - +
501A LEU* 1.3 59.3 + - - +
504A LEU* 2.8 36.5 + - + +
505A CYS* 3.5 8.1 + - - -
1438A THR* 3.0 30.9 - - + +
1143B ALA* 2.6 45.1 - - + +
1145B SER* 2.9 37.1 + - - -
1146B PHE* 3.1 10.9 + - + +
91F ALA* 5.4 5.4 + - + +
92F ARG* 6.3 0.7 - - - -
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Residues in contact with LEU 501 (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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441A PRO* 4.8 6.1 - - + +
442A VAL* 4.4 4.3 - - - -
443A LEU* 3.5 55.0 - - + +
457A ALA* 4.0 10.3 - - + -
492A PRO* 4.0 30.5 - - + -
497A THR* 4.5 4.0 - - + +
498A ARG* 2.4 24.7 + - - +
500A GLU* 1.3 69.9 - - - +
502A SER* 1.3 57.5 + - - +
505A CYS* 2.8 40.5 + - + -
506A ALA 2.9 11.6 + - - -
1143B ALA* 5.9 0.7 - - + -
1146B PHE* 4.2 26.2 - - + -
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Residues in contact with SER 502 (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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441A PRO* 4.5 18.8 - - - +
457A ALA* 5.2 1.3 - - - -
498A ARG* 2.9 5.8 + - - +
499A ALA* 3.2 21.1 + - - -
501A LEU* 1.3 76.9 - - - +
503A GLN* 1.3 76.1 + - - +
506A ALA* 3.8 18.7 - - - +
509A LEU* 4.2 2.9 - - - +
118F LEU* 4.4 10.1 - - - +
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Residues in contact with GLN 503 (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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499A ALA* 2.7 25.4 + - + +
502A SER* 1.3 97.2 + - - +
504A LEU* 1.3 70.1 + - + +
509A LEU* 3.6 15.7 - - - +
87F LYS* 5.6 1.2 - - - +
90F ARG* 2.9 39.8 - - - +
91F ALA* 3.8 19.2 - - + +
94F LEU* 4.3 10.5 - - + +
118F LEU* 4.7 8.5 - - - +
122F MET* 4.7 10.5 - - - -
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Residues in contact with LEU 504 (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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452A LYS* 5.6 0.2 + - - -
500A GLU* 2.8 43.0 + - + +
503A GLN* 1.3 82.9 - - + +
505A CYS* 1.3 67.0 + - - +
506A ALA 3.5 2.0 + - - -
509A LEU* 4.1 9.4 - - - +
510A GLN* 3.4 19.9 + - - -
1438A THR* 4.6 2.0 - - - +
1141B HIS* 3.9 18.8 + - - +
1142B GLY 4.5 6.3 - - - +
1143B ALA* 5.9 1.3 - - + -
87F LYS* 4.6 14.1 - - + +
88F TYR* 3.6 40.2 - - + -
91F ALA* 3.7 25.4 - - + -
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Residues in contact with CYS 505 (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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443A LEU* 4.6 3.1 - - + -
455A MET 4.9 0.3 - - - +
456A MET* 3.7 9.6 - - - +
457A ALA* 2.9 24.0 + - + +
500A GLU 3.5 7.6 + - - -
501A LEU* 2.8 33.7 + - + +
504A LEU* 1.3 80.4 - - - +
506A ALA* 1.3 66.3 + - - +
510A GLN* 4.6 1.5 - - - +
1138B MET* 3.7 29.8 - - - -
1141B HIS* 3.7 29.3 - - + +
1143B ALA* 4.4 5.4 - - - -
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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
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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