Contacts of the helix formed by residues 507 - 518 (chain A) in PDB entry 3NYN
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 VAL 507 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A LEU 5.5 0.2 - - - +
239A GLU* 4.0 33.9 - - + +
249A LEU* 3.0 45.8 - - + +
250A ALA 2.8 20.9 + - - +
251A TYR 4.0 1.1 - - - +
252A ALA* 6.1 0.4 - - + -
504A THR* 6.1 2.0 - - + -
505A GLY 4.4 4.5 - - - +
506A SER* 1.3 70.7 - - - +
508A PRO* 1.3 75.9 - - + +
509A ILE 4.5 0.7 - - - +
510A PRO* 3.4 19.1 - - + +
511A TRP* 2.8 24.0 + - - +
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Residues in contact with PRO 508 (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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60A GLN* 4.6 4.9 - - + +
174A LYS* 4.0 11.0 - - - +
177A GLU* 3.3 34.1 - - - +
178A ARG* 6.3 0.2 - - - +
239A GLU* 6.1 2.0 - - + +
504A THR* 6.4 0.7 - - + -
506A SER 3.3 8.9 - - - +
507A VAL* 1.3 87.4 - - + +
509A ILE* 1.3 67.8 + - + +
511A TRP* 3.6 0.6 - - + +
512A GLN* 2.9 31.8 + - - +
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Residues in contact with ILE 509 (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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59A ARG* 3.5 66.0 - - + +
60A GLN* 4.7 6.1 - - + -
61A PRO* 4.0 16.5 - - + +
242A ASN* 4.5 22.2 - - + +
507A VAL* 4.5 0.6 - - - +
508A PRO* 1.3 81.0 - - + +
510A PRO* 1.3 75.7 - - + +
512A GLN* 3.4 2.6 + - - +
513A ASN* 2.9 40.2 + - - +
582A SO4 4.9 4.5 - - - +
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Residues in contact with PRO 510 (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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210A LYS* 5.6 1.0 + - - -
212A TYR* 4.5 4.1 + - - +
248A SER* 4.7 17.5 - - - +
249A LEU 3.2 28.5 - - - +
250A ALA* 4.0 13.2 - - + -
507A VAL* 3.4 20.0 - - + +
509A ILE* 1.3 95.4 - - + +
511A TRP* 1.3 62.6 + - - +
513A ASN* 3.1 14.0 + - + +
514A GLU* 2.8 22.4 + - - +
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Residues in contact with TRP 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 5.7 2.5 - - + -
62A ILE* 4.3 13.5 - - + -
173A TRP* 3.7 22.7 - + - -
176A LEU* 3.9 14.8 + - + -
177A GLU* 3.3 50.4 - - + +
212A TYR* 5.3 0.2 - - - -
250A ALA* 4.9 4.2 - - - +
251A TYR* 3.2 28.7 + + - -
506A SER* 3.5 28.2 + - - -
507A VAL 2.8 26.3 + - - +
508A PRO* 3.6 3.1 - - + +
510A PRO* 1.3 70.6 - - - +
512A GLN* 1.3 82.6 + - + +
514A GLU* 2.9 27.5 + - - +
515A MET* 3.2 46.1 + - + +
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Residues in contact with GLN 512 (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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60A GLN* 2.6 62.0 + - - +
61A PRO* 3.3 9.2 - - + +
62A ILE* 3.3 32.2 + - + +
63A GLY 4.0 0.8 + - - -
170A PHE* 4.5 4.6 - - - -
174A LYS* 3.7 7.1 - - - +
177A GLU* 3.1 25.5 + - - +
508A PRO* 2.9 15.4 + - - +
509A ILE 3.7 2.9 - - - +
511A TRP* 1.3 85.3 - - + +
513A ASN* 1.3 63.2 + - - +
515A MET* 3.1 14.8 + - - +
516A VAL* 3.2 16.3 + - - +
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Residues in contact with ASN 513 (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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61A PRO* 3.2 21.0 - - - +
210A LYS* 5.6 2.0 - - - +
242A ASN* 5.6 1.0 + - - -
509A ILE* 2.9 43.1 + - - +
510A PRO* 3.1 10.4 + - + +
512A GLN* 1.3 74.3 - - - +
514A GLU* 1.3 64.3 + - - +
516A VAL* 2.9 9.1 + - - +
517A GLU* 2.8 41.3 + - + +
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Residues in contact with GLU 514 (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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205A VAL* 3.4 5.7 - - - +
208A THR* 2.6 36.0 + - - +
210A LYS* 3.6 26.4 - - + +
212A TYR* 2.8 40.7 + - - +
251A TYR* 2.6 30.6 + - - -
510A PRO 2.8 11.4 + - - +
511A TRP* 2.9 15.0 + - - +
513A ASN* 1.3 71.8 - - - +
515A MET* 1.3 63.4 + - + +
517A GLU* 3.2 2.7 + - - +
518A THR* 2.9 29.2 + - - +
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Residues in contact with MET 515 (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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34A LEU* 4.1 24.0 - - + -
62A ILE* 4.3 7.2 - - + -
173A TRP* 4.1 20.4 - - + -
176A LEU* 6.2 0.2 - - - -
205A VAL* 5.8 0.4 - - + -
207A ALA* 5.9 0.2 - - + -
208A THR* 3.5 31.4 - - + -
251A TYR* 4.8 1.3 - - - +
511A TRP* 3.3 62.6 - - + +
512A GLN 3.1 6.8 + - - +
514A GLU* 1.3 82.8 - - - +
516A VAL* 1.3 58.9 + - - +
518A THR* 3.4 5.4 + - - -
520A CYS* 3.0 32.6 + - - -
521A PHE* 3.1 9.5 + - + +
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Residues in contact with VAL 516 (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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61A PRO* 5.2 4.9 - - + -
62A ILE* 4.0 23.1 - - + +
65A LEU* 4.2 18.8 - - + -
512A GLN 3.2 14.3 + - - +
513A ASN* 2.9 9.5 + - - +
515A MET* 1.3 73.5 - - - +
517A GLU* 1.3 67.6 + - + +
519A GLU* 3.3 14.1 + - - +
521A PHE* 4.1 16.2 - - + -
522A GLN 5.8 0.2 - - - +
534B PRO* 4.2 26.7 - - + -
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Residues in contact with GLU 517 (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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210A LYS* 2.9 39.6 + - - +
513A ASN* 2.8 28.4 + - + +
514A GLU 3.6 4.3 - - - +
516A VAL* 1.3 80.1 - - + +
518A THR* 1.3 60.6 + - + +
519A GLU* 3.2 9.5 + - - +
545B ALA 3.8 18.0 - - - +
546B PRO* 6.0 1.6 - - - -
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Residues in contact with THR 518 (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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26A LYS* 3.8 13.2 - - - -
208A THR* 3.5 33.3 - - - +
209A GLY 5.2 0.2 - - - -
210A LYS* 4.0 24.5 - - + +
514A GLU* 2.9 19.6 + - + +
515A MET* 3.4 3.8 + - - -
516A VAL 3.2 0.4 - - - -
517A GLU* 1.3 79.5 - - + +
519A GLU* 1.3 58.2 + - - +
520A CYS* 2.7 38.8 + - - +
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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