Contacts of the helix formed by residues 513 - 527 (chain D) in PDB entry 1NLW
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 ARG 513 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509D MET 2.9 18.4 + - - +
510D GLU* 2.9 41.8 + - - +
512D ASN* 1.3 78.1 - - - +
514D ARG* 1.3 67.4 + - - +
516D HIS* 3.5 5.8 + - - +
517D LEU* 3.2 49.5 + - + +
740E ALA* 6.3 0.4 - - - +
806J A 4.7 3.6 - - - -
807J G 3.7 61.3 + - - +
808J C 3.6 23.6 + - - -
809J A 5.1 2.0 + - - +
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Residues in contact with ARG 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510D GLU* 2.7 56.4 + - - +
511D LYS* 3.2 33.5 - - - +
513D ARG* 1.3 78.1 - - - +
515D ALA* 1.3 57.5 + - - +
517D LEU* 3.1 12.6 + - + +
518D ARG* 2.9 43.2 + - - +
609H A 4.1 3.8 - - - +
610H C 3.1 68.4 + - - +
611H G 3.5 19.6 + - - -
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Residues in contact with ALA 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511D LYS 2.8 17.2 + - - +
512D ASN* 3.6 8.7 - - - +
513D ARG 3.3 0.4 - - - -
514D ARG* 1.3 77.8 - - - +
516D HIS* 1.3 61.1 + - - +
518D ARG* 3.1 22.3 + - - +
519D LEU* 3.1 25.7 + - - +
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Residues in contact with HIS 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512D ASN 3.0 16.5 + - - +
513D ARG* 3.8 5.8 + - - +
515D ALA* 1.3 76.9 - - - +
517D LEU* 1.3 68.6 + - - +
519D LEU* 3.3 16.5 + - + +
520D SER* 3.1 40.7 + - - -
740E ALA* 4.4 13.3 - - + +
744E ASP* 4.0 15.3 + - - -
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Residues in contact with LEU 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D ARG* 3.2 39.7 + - + +
514D ARG* 3.1 14.9 + - + +
516D HIS* 1.3 80.6 + - + +
518D ARG* 1.3 67.5 + - - +
520D SER* 3.2 3.8 + - - +
521D LEU* 2.9 25.6 + - - +
722E PHE* 5.9 1.8 - - + -
739E ARG* 4.1 22.9 - - + -
740E ALA* 3.5 43.1 - - + +
743E LEU* 3.9 13.9 - - + +
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Residues in contact with ARG 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511D LYS 4.7 1.4 + - - -
514D ARG* 2.9 25.2 + - + +
515D ALA* 3.1 43.9 - - - +
517D LEU* 1.3 78.0 - - - +
519D LEU* 1.3 58.5 + - + +
521D LEU* 3.4 9.6 + - + +
522D GLU* 3.0 28.9 + - - +
609H A 3.3 51.4 + - - +
610H C 2.7 30.9 + - - -
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Residues in contact with LEU 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515D ALA* 3.1 17.0 + - + +
516D HIS* 3.5 16.6 - - + +
517D LEU 3.2 0.2 - - - -
518D ARG* 1.3 75.0 - - + +
520D SER* 1.3 66.7 + - - +
522D GLU* 3.2 14.4 + - + +
523D LYS* 2.9 24.5 + - - +
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Residues in contact with SER 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D HIS* 3.1 27.5 + - - -
517D LEU* 3.7 8.5 - - - -
519D LEU* 1.3 74.5 - - - +
521D LEU* 1.3 63.0 + - - +
523D LYS* 3.3 9.3 + - - +
524D LEU* 3.0 22.3 + - - +
740E ALA 5.2 0.7 - - - -
743E LEU* 3.7 23.8 - - - +
744E ASP* 2.8 28.1 + - - -
747E THR* 4.7 2.8 + - - -
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Residues in contact with LEU 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D LEU 2.9 17.9 + - - +
518D ARG* 3.5 9.9 - - + +
519D LEU 3.1 0.2 - - - -
520D SER* 1.3 77.1 - - - +
522D GLU* 1.3 57.9 + - - +
524D LEU* 3.1 7.4 + - + +
525D LYS 2.9 24.4 + - - -
539D THR* 3.4 35.4 - - + +
542D LEU* 3.5 35.9 - - + +
543D LEU* 4.7 9.9 - - + -
722E PHE* 5.7 2.5 - - + -
743E LEU* 3.8 26.6 - - + +
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Residues in contact with GLU 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D ARG 3.0 16.9 + - - +
519D LEU* 3.2 14.4 + - + +
521D LEU* 1.3 76.3 - - - +
523D LYS* 1.3 62.7 + - - +
525D LYS* 3.2 25.8 + - - +
526D GLY* 3.2 17.7 + - - -
535D SER* 5.4 3.3 + - - -
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Residues in contact with LYS 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519D LEU 2.9 16.9 + - - +
520D SER* 3.6 8.3 - - - +
521D LEU 3.2 0.2 - - - -
522D GLU* 1.3 76.9 - - - +
524D LEU* 1.3 62.9 + - - +
526D GLY* 3.4 9.1 + - - -
527D LEU* 3.5 17.2 + - + +
747E THR* 4.0 25.9 - - + +
751E GLN* 4.6 12.5 - - - +
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Residues in contact with LEU 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D SER 3.0 13.1 + - - +
521D LEU* 3.1 10.7 + - + +
523D LYS* 1.3 74.1 - - - +
525D LYS* 1.3 66.0 + - - +
527D LEU* 3.0 16.8 + - + +
528D VAL* 3.1 23.6 + - + +
542D LEU* 4.6 9.6 - - + -
543D LEU* 5.2 1.8 - - + -
546D ALA* 4.0 22.9 - - + -
725E LEU* 4.3 10.1 - - + -
743E LEU* 4.1 30.3 - - + +
746E ALA* 4.7 2.7 - - + -
747E THR* 4.0 22.4 + - - +
750E ILE* 3.7 31.4 - - + -
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Residues in contact with LYS 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D LEU 2.9 12.6 + - - +
522D GLU* 3.4 29.8 - - - +
524D LEU* 1.3 77.9 - - - +
526D GLY* 1.3 62.0 + - - +
528D VAL* 3.3 13.2 + - - +
531D GLY 3.6 12.8 + - - +
532D PRO* 3.6 19.6 + - - +
533D ASP* 4.0 3.8 - - - +
534D SER* 2.8 48.4 + - - +
535D SER* 4.4 11.5 + - - +
537D HIS* 5.1 8.3 - - + +
542D LEU* 3.6 28.2 - - + +
545D LYS* 4.9 4.2 + - - +
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Residues in contact with GLY 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522D GLU 3.2 9.3 + - - -
523D LYS* 3.4 4.9 + - - -
524D LEU 3.1 1.0 - - - -
525D LYS* 1.3 82.0 - - - +
527D LEU* 1.3 61.0 + - - +
528D VAL 3.2 0.7 - - - -
532D PRO* 3.4 32.0 - - - +
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Residues in contact with LEU 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523D LYS* 3.5 12.3 + - + +
524D LEU* 3.0 12.5 + - + +
526D GLY* 1.3 80.0 - - - +
528D VAL* 1.3 60.4 + - - +
529D PRO* 3.1 13.1 - - - +
549D HIS* 3.8 10.6 + - - -
747E THR* 3.4 37.2 - - + +
750E ILE* 4.1 15.3 - - + +
751E GLN* 3.4 28.7 - - + +
754E ARG* 3.0 36.1 + - - +
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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