Contacts of the helix formed by residues 524 - 540 (chain A) in PDB entry 4RM9
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 ASN 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A GLU* 3.7 8.7 + - - -
193A LYS* 4.6 2.8 - - - +
520A GLU* 2.7 39.4 + - - +
521A ALA 3.2 7.9 - - - +
522A GLU 3.5 0.2 - - - -
523A LYS* 1.3 79.5 - - + +
525A GLU* 1.3 63.1 + - - +
526A ARG* 3.1 20.2 + - - +
527A VAL* 3.1 24.5 + - + +
528A GLN 3.0 17.5 + - - -
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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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521A ALA 4.6 0.9 - - - +
522A GLU 5.6 3.8 - - - +
523A LYS 4.0 3.3 + - - +
524A ASN* 1.3 72.7 + - - +
526A ARG* 1.3 57.6 + - - +
528A GLN* 3.4 18.5 + - - +
529A ARG* 3.0 28.9 + - - +
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Residues in contact with ARG 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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128A TYR* 5.3 1.9 + - - +
178A GLU* 2.9 47.7 + - - +
179A HIS* 5.1 1.4 + - - +
182A MET* 5.7 7.3 - - - +
524A ASN* 3.1 10.6 + - - +
525A GLU* 1.3 75.0 - - - +
527A VAL* 1.3 66.0 + - + +
529A ARG* 3.3 8.3 + - + +
530A GLN* 3.1 45.5 + - + +
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Residues in contact with VAL 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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124A LEU* 4.2 4.7 - - + -
128A TYR* 4.0 15.0 - - - +
190A GLU* 3.3 29.2 - - - +
194A ILE* 4.0 24.2 - - + -
520A GLU* 4.4 3.4 - - + +
521A ALA* 4.5 9.4 - - - +
524A ASN* 3.1 27.7 + - + +
526A ARG* 1.3 77.8 - - + +
528A GLN* 1.3 64.3 + - - +
530A GLN* 3.1 8.9 + - - +
531A LEU* 3.0 38.9 + - + +
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Residues in contact with GLN 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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521A ALA* 3.3 41.3 + - + +
522A GLU* 4.2 14.3 + - - +
524A ASN 3.0 6.9 + - - +
525A GLU* 3.5 19.8 - - - +
527A VAL* 1.3 78.4 - - - +
529A ARG* 1.3 60.8 + - - +
531A LEU* 3.5 5.2 + - + +
532A LEU* 3.1 43.8 + - + +
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Residues in contact with ARG 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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175A TRP* 5.7 4.8 - - - -
178A GLU* 5.6 3.6 + - - -
525A GLU 3.0 16.5 + - - +
526A ARG* 3.7 7.6 - - - +
527A VAL 3.2 0.2 - - - -
528A GLN* 1.3 76.5 - - - +
530A GLN* 1.3 58.8 + - + +
532A LEU* 3.5 8.6 + - + +
533A THR* 2.8 48.1 + - - +
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Residues in contact with GLN 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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124A LEU* 3.4 30.7 - - + +
128A TYR* 2.8 29.1 + - - -
175A TRP* 3.7 24.9 - - + -
178A GLU* 4.7 5.6 + - - +
179A HIS* 3.8 14.2 + - - -
526A ARG* 3.1 44.5 + - + +
527A VAL* 3.1 11.1 + - - +
529A ARG* 1.3 74.8 - - + +
531A LEU* 1.3 61.1 + - - +
533A THR* 3.3 2.6 + - - -
534A LEU* 2.8 35.5 + - - +
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Residues in contact with LEU 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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120A GLU* 4.1 7.9 - - + +
121A THR* 3.9 37.9 - - + +
124A LEU* 3.8 20.2 - - + -
194A ILE* 5.6 5.6 - - + -
521A ALA* 4.0 22.0 - - + -
527A VAL* 3.0 28.6 + - + +
528A GLN* 3.8 5.4 - - - +
530A GLN* 1.3 75.5 - - - +
532A LEU* 1.3 60.9 + - + +
534A LEU* 3.1 7.3 + - - +
535A SER* 2.9 33.5 + - - +
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Residues in contact with LEU 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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528A GLN* 3.1 35.5 + - + +
529A ARG* 3.8 7.0 - - + +
531A LEU* 1.3 78.7 - - + +
533A THR* 1.3 62.8 + - - +
535A SER* 3.4 11.4 + - - +
536A SER* 3.1 21.7 + - - -
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Residues in contact with THR 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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175A TRP* 3.5 26.5 - - + -
529A ARG* 2.8 40.6 + - - +
530A GLN 3.6 3.8 - - - -
532A LEU* 1.3 72.2 - - - +
534A LEU* 1.3 66.6 + - - +
536A SER* 3.2 9.4 + - - -
537A GLU* 3.0 34.2 + - + +
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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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120A GLU* 3.8 27.8 - - + +
123A VAL* 4.1 17.5 - - + -
124A LEU* 4.2 20.0 - - + -
171A ARG* 5.9 2.5 - - + +
175A TRP* 3.3 48.7 - - + +
530A GLN 2.8 26.8 + - - +
531A LEU* 3.1 9.2 + - - +
533A THR* 1.3 75.9 - - - +
535A SER* 1.3 64.9 + - - +
537A GLU* 2.9 13.2 + - - +
538A LEU* 2.9 36.9 + - + +
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Residues in contact with SER 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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120A GLU* 3.1 31.7 - - - +
531A LEU* 2.9 17.0 + - - +
532A LEU* 3.6 16.4 - - - +
534A LEU* 1.3 72.2 - - - +
536A SER* 1.3 62.8 + - - +
539A SER* 3.1 31.5 + - - -
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Residues in contact with SER 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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532A LEU 3.1 13.8 + - - -
533A THR* 3.3 14.1 - - - -
534A LEU 3.1 0.4 + - - -
535A SER* 1.3 79.6 - - - +
537A GLU* 1.3 64.3 + - - +
538A LEU 3.3 0.3 + - - -
539A SER* 3.8 9.6 + - - -
540A GLN* 4.4 7.4 + - - +
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Residues in contact with GLU 537 (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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171A ARG* 3.4 39.7 + - - +
174A VAL* 5.2 7.6 - - - +
175A TRP* 3.4 28.3 + - - -
533A THR* 3.0 34.3 + - + +
534A LEU* 2.9 13.3 + - - +
536A SER* 1.3 78.1 - - - +
538A LEU* 1.3 61.4 + - + +
540A GLN* 4.2 11.1 + - - +
541A ALA 4.8 0.7 + - - -
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Residues in contact with LEU 538 (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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119A PRO 4.6 1.8 - - - -
120A GLU* 3.9 36.1 - - + +
123A VAL* 4.0 24.7 - - + -
161A HIS* 3.9 19.9 - - + +
163A LEU* 4.5 4.9 - - + -
168A TRP* 4.1 24.0 - - + -
171A ARG* 3.2 26.9 - - + +
534A LEU* 2.9 26.9 + - + +
537A GLU* 1.3 77.1 - - - +
539A SER* 1.3 56.4 + - - +
540A GLN 3.0 3.1 - - - -
541A ALA* 2.7 28.8 + - + +
542A ARG* 3.1 9.2 + - - -
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Residues in contact with SER 539 (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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120A GLU* 5.0 2.5 + - - -
535A SER* 3.1 19.7 + - - -
536A SER* 3.8 5.6 + - - -
537A GLU 3.7 0.4 - - - -
538A LEU* 1.3 75.5 - - - +
540A GLN* 1.3 63.8 + - - +
541A ALA 3.3 0.7 + - - -
542A ARG* 3.4 33.4 + - - +
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Residues in contact with GLN 540 (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 LYS* 5.5 4.3 + - - +
171A ARG* 6.3 0.2 - - - +
536A SER 4.4 6.7 + - - +
537A GLU 4.2 9.3 + - - +
538A LEU 2.9 1.0 + - - -
539A SER* 1.3 82.2 - - - +
541A ALA* 1.3 58.3 + - + +
542A ARG 3.5 0.4 - - - -
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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