Contacts of the helix formed by residues 524 - 536 (chain A) in PDB entry 6CNB
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 THR 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A PRO* 5.6 0.2 - - - -
523A GLN* 1.3 81.5 - - - +
525A GLU* 1.3 70.2 + - - +
526A GLU* 4.0 14.6 + - + +
527A ALA* 2.9 38.6 + - + +
528A ARG* 3.5 8.3 + - - +
1077B GLN* 5.1 2.9 - - - +
1081B GLU* 4.0 15.2 - - + +
1085B ILE* 5.7 11.2 - - + -
99F LEU* 4.3 11.8 - - - +
62G GLY 5.2 3.5 + - - -
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Residues in contact with GLU 525 (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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404A TYR* 2.5 37.0 + - - -
405A PRO 3.6 9.2 - - - +
406A GLU* 3.7 12.9 - - - +
407A LYS* 4.9 7.8 + - + +
523A GLN 3.6 1.0 + - - +
524A THR* 1.3 74.7 + - - +
526A GLU* 1.3 59.6 + - - +
528A ARG* 3.5 25.3 + - - +
529A ALA* 3.9 6.8 + - - +
95F GLY 4.9 2.6 - - - +
98F ALA* 5.1 5.0 - - + +
99F LEU* 4.2 25.8 - - + +
102F SER* 3.9 20.2 - - - +
117F PRO* 3.2 28.2 - - - +
118F LEU* 4.7 1.6 - - - +
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Residues in contact with GLU 526 (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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524A THR* 4.0 16.3 + - + +
525A GLU* 1.3 76.8 - - - +
527A ALA* 1.3 64.6 + - - +
528A ARG 3.4 0.7 - - - -
529A ALA 4.1 1.2 - - - -
530A GLU* 3.2 19.8 + - - +
1077B GLN* 3.3 33.5 - - + +
92F ARG* 4.7 3.8 + - - +
95F GLY* 3.8 29.4 - - - +
96F THR* 4.0 19.1 + - - -
99F LEU* 4.3 15.0 - - + +
61G PRO 2.8 27.5 - - - +
62G GLY* 3.8 10.6 - - - +
63G ASP 5.3 0.3 - - - +
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Residues in contact with ALA 527 (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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522A PRO* 4.0 15.8 - - + +
524A THR* 2.9 24.4 + - + +
526A GLU* 1.3 80.9 - - - +
528A ARG* 1.3 68.2 + - - +
530A GLU* 3.1 9.8 - - - +
531A ALA* 2.9 18.9 + - - +
1077B GLN* 4.1 10.3 - - - +
1078B LEU* 4.5 10.1 - - + +
1081B GLU* 3.8 18.8 - - + -
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Residues in contact with ARG 528 (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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404A TYR* 3.0 44.2 + - + -
469A GLY 4.6 5.9 + - - -
470A ASP* 4.8 9.2 + - - +
471A VAL* 4.2 39.3 - - + +
522A PRO* 4.2 17.8 - - + +
524A THR 3.5 5.4 + - - +
525A GLU* 3.5 23.5 + - - +
527A ALA* 1.3 75.0 - - - +
529A ALA* 1.3 55.9 + - - +
531A ALA* 2.3 38.7 + - - +
532A ILE* 3.3 5.9 + - - +
116F ASP* 4.9 10.9 + - - +
117F PRO* 4.6 3.6 - - - +
118F LEU* 3.4 43.4 - - + +
119F ARG* 5.3 4.6 - - - +
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Residues in contact with ALA 529 (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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525A GLU 3.9 5.4 + - - +
526A GLU 3.9 0.6 + - - +
527A ALA 3.5 0.2 - - - -
528A ARG* 1.3 77.0 - - - +
530A GLU* 1.3 59.4 + - - +
532A ILE* 4.9 3.6 - - - -
533A ASN* 3.1 28.2 + - - +
91F ALA* 4.5 5.5 - - - +
94F LEU* 4.1 10.1 - - + -
95F GLY* 3.6 35.0 - - - +
98F ALA* 5.1 0.4 - - + -
118F LEU* 3.3 29.4 - - + +
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Residues in contact with GLU 530 (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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526A GLU 3.2 16.0 + - - +
527A ALA* 3.1 16.3 + - - +
528A ARG 2.8 1.0 + - - -
529A ALA* 1.3 77.7 - - - +
531A ALA* 1.3 61.5 + - - +
534A LEU* 3.3 34.6 + - - +
535A MET* 3.6 3.0 + - + +
1425A THR* 3.0 36.4 + - - +
1075B ALA* 3.1 37.2 - - + +
1077B GLN* 4.7 8.6 - - + +
1078B LEU* 4.4 14.4 - - + +
91F ALA* 3.6 15.1 + - - +
92F ARG* 4.6 1.7 + - - -
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Residues in contact with ALA 531 (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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471A VAL* 3.9 13.7 - - + -
473A LEU* 4.8 11.7 - - + -
487A SER* 3.2 14.6 - - - -
522A PRO* 4.7 10.3 - - + -
527A ALA 2.9 10.2 + - - +
528A ARG* 2.3 26.5 + - - +
530A GLU* 1.3 64.9 - - - +
532A ILE* 1.3 64.4 + - - +
533A ASN 3.1 0.2 + - - -
535A MET* 2.7 38.1 + - + -
536A GLY 2.9 3.5 + - - -
1078B LEU* 5.3 3.8 - - + -
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Residues in contact with ILE 532 (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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390A ASP* 5.3 2.7 - - + -
471A VAL* 3.6 31.7 - - + +
487A SER* 3.3 28.2 + - - +
488A HIS* 4.7 0.2 - - - -
489A TYR* 3.3 48.0 - - + +
528A ARG 3.3 6.4 + - - +
529A ALA* 4.9 5.6 - - - -
531A ALA* 1.3 79.8 - - - +
533A ASN* 1.3 70.2 + - + +
536A GLY* 3.3 17.1 - - - -
537A VAL 4.8 1.8 - - - +
538A LYS* 4.6 11.9 - - - +
539A ASN* 6.0 0.2 - - - +
118F LEU* 5.0 10.3 - - + -
122F MET* 6.1 3.4 - - + -
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Residues in contact with ASN 533 (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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529A ALA* 3.1 16.7 + - - +
531A ALA 3.2 1.0 - - - -
532A ILE* 1.3 89.2 - - + +
534A LEU* 1.3 60.2 + - - +
539A ASN* 3.5 26.0 + - - +
87F LYS 5.1 1.6 + - - -
90F ARG* 3.3 57.7 + - - +
91F ALA* 3.4 10.7 - - - +
94F LEU* 4.4 14.8 - - + +
118F LEU* 6.6 0.4 - - + -
122F MET* 5.0 10.1 - - + +
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Residues in contact with LEU 534 (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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482A ARG* 5.7 0.7 - - - +
530A GLU* 3.3 36.8 + - - +
531A ALA 3.3 1.0 + - - -
533A ASN* 1.3 79.8 - - - +
535A MET* 1.3 55.7 + - + +
536A GLY 3.2 4.9 + - - +
539A ASN* 4.6 6.4 - - - +
540A ASN* 2.8 25.8 + - - +
1425A THR* 4.5 0.9 - - - +
1073B TYR* 3.3 35.0 - - + +
1075B ALA* 4.6 2.5 - - + +
87F LYS* 3.6 45.7 - - + +
88F TYR* 3.8 16.6 - - + -
91F ALA* 4.4 12.8 - - + -
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Residues in contact with MET 535 (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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473A LEU* 4.9 4.7 - - - -
485A ILE* 3.5 29.2 - - + +
486A LEU* 3.7 9.9 - - - +
487A SER* 3.5 11.7 + - - +
530A GLU 4.3 2.0 - - - +
531A ALA* 2.7 23.3 + - - +
534A LEU* 1.3 72.4 - - + +
536A GLY* 1.3 65.6 + - - +
540A ASN* 3.4 8.3 + - - +
1070B VAL* 3.6 25.8 - - + -
1073B TYR* 3.5 49.1 - - + -
1075B ALA* 4.0 11.2 - - + -
1078B LEU* 3.5 22.9 - - + -
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Residues in contact with GLY 536 (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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486A LEU* 5.0 1.1 - - - +
487A SER* 3.0 22.0 - - - -
531A ALA 2.9 5.5 + - - -
532A ILE* 3.3 18.0 + - - -
533A ASN 4.5 0.2 - - - -
534A LEU 3.2 5.0 + - - +
535A MET* 1.3 83.0 - - - +
537A VAL* 1.3 66.1 + - - -
538A LYS 3.7 0.9 - - - -
539A ASN* 4.8 2.2 - - - +
540A ASN* 3.0 21.7 + - - +
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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