Contacts of the helix formed by residues 312 - 318 (chain A) in PDB entry 2NUP
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 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A ILE 4.9 2.0 - - - -
311A ARG* 1.3 76.6 - - - +
313A TRP* 1.3 64.7 + - - +
314A HIS* 3.3 13.6 + - - +
315A ASP* 2.8 43.3 + - - +
316A ILE* 3.0 12.6 + - - +
354A GLN* 4.8 0.7 - - - +
597A PRO* 4.1 10.3 - - - -
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Residues in contact with TRP 313 (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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312A SER* 1.3 73.0 - - - +
314A HIS* 1.3 63.0 + - + +
316A ILE* 2.7 51.1 - - + +
317A ASP* 2.9 9.2 + - - +
358A LEU* 4.2 21.3 - - + -
361A LYS* 5.9 0.2 - - - -
592A VAL* 3.4 36.1 - - + +
593A PHE* 3.9 23.9 - + + -
595A ASN 3.0 26.4 + - - +
597A PRO* 3.3 45.4 - - + +
600A SER* 3.0 33.4 + - - -
601A SER* 5.2 1.3 - - - -
604A ARG* 5.7 5.6 - - - -
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Residues in contact with HIS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A SER* 3.1 10.9 + - - +
313A TRP* 1.3 76.9 - - + +
315A ASP* 1.3 65.0 + - - +
317A ASP* 3.0 6.7 + - - +
318A LYS* 3.0 42.7 + - + +
593A PHE* 3.7 35.0 - + + +
594A ASN 5.6 2.7 + - - -
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Residues in contact with ASP 315 (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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309A PRO* 5.4 6.3 - - - +
310A ILE 4.4 3.3 - - - +
311A ARG* 4.0 10.6 - - + -
312A SER* 2.8 37.3 + - - +
314A HIS* 1.3 79.2 - - - +
316A ILE* 1.3 61.6 + - - +
318A LYS* 3.2 8.8 + - - -
320A ASN* 2.9 64.6 + - - +
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Residues in contact with ILE 316 (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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311A ARG* 5.7 2.2 - - + -
312A SER 3.0 10.0 + - - +
313A TRP* 2.7 60.1 - - + +
315A ASP* 1.3 76.1 - - - +
317A ASP* 1.3 64.0 + - + +
319A ASP* 3.5 13.2 + - - +
320A ASN 4.9 0.2 - - - +
321A ALA* 4.3 12.0 - - + +
324A VAL* 5.0 23.3 - - + -
325A LYS* 6.3 2.7 - - - -
358A LEU* 5.6 3.1 - - + -
593A PHE* 6.0 0.4 - - + -
597A PRO* 6.0 1.1 - - + -
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Residues in contact with ASP 317 (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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313A TRP 2.9 12.0 + - - +
314A HIS* 3.0 9.6 + - - +
316A ILE* 1.3 84.7 - - + +
318A LYS* 1.3 60.1 + - + +
319A ASP* 3.2 12.4 + - - +
593A PHE* 3.6 24.2 - - + -
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Residues in contact with LYS 318 (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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314A HIS* 3.0 32.8 + - + +
315A ASP* 3.2 3.1 + - - +
317A ASP* 1.3 81.2 - - + +
319A ASP* 1.3 74.0 + - - +
320A ASN* 3.1 11.7 + - + +
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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