Contacts of the strand formed by residues 344 - 348 (chain D) in PDB entry 1C7G
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 ALA 344 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D GLY 3.9 4.7 + - - +
322D VAL* 3.8 10.8 - - - +
340D THR* 4.0 0.5 - - - +
341D GLY 3.7 21.0 + - - -
343D HIS* 1.3 93.3 + - + +
345D VAL* 1.3 64.7 + - - +
346D PHE* 4.1 19.5 - - + -
404D ARG* 4.2 3.8 - - + -
405D LEU 3.4 14.6 - - - +
406D THR* 3.5 18.6 - - + -
407D ILE* 4.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D VAL* 3.8 25.1 - - + +
325D LEU* 4.0 18.4 - - + -
326D GLY* 4.0 14.6 - - - +
329D LEU* 3.9 26.0 - - + -
336D ILE* 4.2 17.3 - - + -
340D THR* 3.9 13.0 - - + +
344D ALA* 1.3 78.2 - - - +
346D PHE* 1.3 65.3 + - - +
347D LEU* 4.6 0.2 - - + -
403D VAL 3.8 1.0 - - - +
404D ARG* 3.8 0.9 - - - -
405D LEU* 2.9 40.9 + - + +
407D ILE* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 346 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D ASN* 4.5 13.9 - - - -
186D LEU* 5.5 4.3 - - - -
188D GLY* 3.3 39.7 - - - -
336D ILE* 3.1 6.8 - - - +
337D VAL* 2.9 55.1 + - + +
343D HIS* 5.4 1.6 - - - -
344D ALA* 4.1 15.0 - - + -
345D VAL* 1.3 82.7 - - - +
347D LEU* 1.3 61.3 + - - +
381D ARG* 4.6 7.6 - - + -
400D LEU* 6.2 2.7 - - + -
402D THR* 3.6 25.8 - - + -
403D VAL 3.6 2.7 - - - -
404D ARG* 3.7 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D LEU* 3.8 19.5 - - + -
334D VAL* 3.9 15.7 - - + -
335D PRO 3.6 2.9 - - - +
336D ILE* 3.7 22.7 - - + -
337D VAL* 5.3 0.4 - - - -
345D VAL* 4.6 0.2 - - + -
346D PHE* 1.3 73.8 - - - +
348D ASP* 1.3 60.3 + - - +
349D ALA 3.3 0.4 + - - -
352D PHE* 4.7 3.4 - - + -
366D LEU* 4.0 19.1 - - + -
370D ILE* 3.9 27.4 - - + -
402D THR* 3.0 30.4 - - - -
403D VAL* 2.9 21.9 + - + +
405D LEU* 4.0 18.8 - - + -
424D ILE* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ALA* 5.9 2.4 - - - +
335D PRO* 2.7 26.0 + - + +
336D ILE* 4.6 4.5 - - - +
337D VAL* 5.6 2.9 - - + +
346D PHE 4.0 0.4 + - - -
347D LEU* 1.3 68.4 - - - +
349D ALA* 1.3 57.3 + - - +
350D ARG* 3.0 24.9 + - - +
351D ARG* 3.0 41.2 + - + +
352D PHE* 2.8 28.8 + - - +
400D LEU* 6.5 0.4 - - - -
401D GLU 3.8 7.4 + - - +
402D THR* 4.5 6.3 - - + -
----------------------------------------------------------
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