Contacts of the helix formed by residues 338 - 347 (chain A) in PDB entry 4U7C
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 338 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 3.8 5.4 - - - -
336A LEU* 2.6 38.2 + - - +
337A PRO* 1.3 75.0 - - - +
339A ARG* 1.3 66.7 + - - +
340A GLN* 3.1 11.0 - - + +
341A ALA* 2.9 44.0 + - - +
342A VAL* 3.3 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 2.6 44.7 + - - +
97A ARG* 4.1 17.3 - - - +
99A LEU* 3.5 15.3 - - + +
338A ASN* 1.3 72.0 - - - +
340A GLN* 1.3 62.3 + - - +
342A VAL* 3.4 11.1 + - - +
343A MET* 2.9 62.7 + - + +
400A LEU* 6.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ASN* 3.0 9.5 + - + +
339A ARG* 1.3 85.3 + - - +
341A ALA* 1.3 57.2 + - - +
343A MET* 3.3 9.0 + - - +
344A ASP* 2.7 71.1 + - - +
347A LYS* 4.3 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ILE* 4.2 9.4 - - + -
336A LEU* 3.5 23.8 - - + +
338A ASN* 2.9 28.7 + - - +
340A GLN* 1.3 73.4 - - - +
342A VAL* 1.3 66.7 + - - +
344A ASP* 3.2 9.2 + - - +
345A PHE* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG* 3.8 22.0 - - - +
99A LEU* 4.3 14.8 - - + -
315A PRO* 4.5 2.0 - - + -
319A LEU* 3.9 25.5 - - + +
335A ILE* 4.0 19.2 - - + +
336A LEU 4.8 0.9 - - - +
338A ASN 3.5 15.0 - - - +
339A ARG* 3.4 12.6 - - - +
341A ALA* 1.3 77.0 - - - +
343A MET* 1.3 59.1 + - + +
345A PHE* 3.2 3.4 + - - +
346A ILE* 2.9 49.7 + - + +
400A LEU 4.3 0.4 - - - +
401A GLY* 4.1 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 4.3 0.9 - - - +
97A ARG* 3.2 38.1 - - - +
339A ARG* 2.9 59.8 + - - +
340A GLN* 3.6 13.7 - - - +
342A VAL* 1.3 76.0 - - + +
344A ASP* 1.3 57.1 + - - +
346A ILE* 3.7 13.7 - - - +
347A LYS* 2.9 37.9 + - - +
399A SER 5.0 4.5 - - - +
400A LEU* 3.5 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLN* 2.7 51.6 + - - +
341A ALA* 3.2 8.6 + - - +
343A MET* 1.3 72.7 - - - +
345A PHE* 1.3 67.0 + - - +
347A LYS* 3.0 40.3 + - + +
348A ASP* 4.6 0.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.4 11.2 - - + -
322A VAL* 3.9 33.7 - - + -
323A CYS* 4.4 11.9 - - - -
326A LYS* 3.5 35.0 - - + -
333A TYR* 3.8 24.7 - + - -
335A ILE* 3.4 32.8 - - + -
341A ALA 2.9 17.3 + - - +
342A VAL 3.5 3.8 - - - +
344A ASP* 1.3 79.9 - - - +
346A ILE* 1.3 66.1 + - - +
348A ASP* 4.1 1.7 + - - +
349A LEU* 3.8 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A MET* 5.9 1.1 - - + -
319A LEU* 4.6 10.8 - - + -
342A VAL* 2.9 26.6 + - + +
343A MET* 3.7 12.1 - - - +
345A PHE* 1.3 75.9 - - + +
347A LYS* 1.3 58.5 + - - +
348A ASP 2.6 5.7 + - - -
349A LEU* 2.6 41.9 + - + +
373A CYS* 3.5 30.2 - - + +
374A THR* 5.3 0.4 - - - +
398A ILE 4.0 5.8 - - - +
399A SER 4.2 9.6 - - - +
400A LEU 3.8 5.8 - - - -
401A GLY* 3.3 40.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLN* 4.3 5.3 - - - +
343A MET* 2.9 25.9 + - - +
344A ASP* 3.0 42.1 + - + +
346A ILE* 1.3 73.9 - - - +
348A ASP* 1.3 82.3 + - + +
349A LEU 3.6 0.2 - - - -
372A THR* 3.7 5.5 + - - -
374A THR* 2.5 35.3 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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