Contacts of the strand formed by residues 334 - 339 (chain C) in PDB entry 3TMP
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 HIS 334 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLN* 6.1 0.7 - - + -
217C GLN* 4.6 3.6 + - - -
218C MET 3.4 19.3 + - - -
220C GLU* 3.5 44.2 + - + +
224C CYS* 3.6 7.4 - - + -
328C SER 3.5 0.5 - - - +
329C TYR* 3.4 6.4 - - - -
330C HIS* 2.8 41.8 + + - +
331C ARG* 4.1 11.9 - - - +
333C ILE* 1.3 79.9 - - - +
335C TYR* 1.3 78.7 + - - +
336C ASN* 2.9 34.4 + - - -
76D GLZ 2.7 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C MET* 3.6 9.5 - - - +
224C CYS* 3.4 12.3 - - - +
225C LEU* 3.9 41.3 - - + -
228C ALA* 4.5 3.1 - - + -
280C GLY 4.8 1.8 - - - -
285C MET* 3.7 25.7 - - + +
298C VAL* 4.3 3.4 - - + -
327C VAL* 3.8 17.9 - - + -
328C SER 3.2 14.8 - - - -
329C TYR* 3.5 29.0 - + + -
334C HIS* 1.3 95.9 + - - +
336C ASN* 1.3 62.1 + - - +
73D LEU* 2.7 46.3 + - - +
75D GLY* 3.7 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ILE* 3.7 10.5 - - + +
216C LYS 3.4 7.6 - - - +
217C GLN* 2.8 29.2 + - - +
218C MET* 2.8 30.4 + - - +
228C ALA* 3.6 5.8 - - - +
327C VAL* 3.3 10.4 - - - +
328C SER* 2.9 40.4 + - - +
330C HIS* 3.3 24.5 + - - -
334C HIS* 2.9 20.2 + - - -
335C TYR* 1.3 72.2 - - - +
337C SER* 1.3 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ILE* 3.6 2.8 - - - -
216C LYS* 2.7 38.2 + - - +
218C MET* 3.7 21.9 - - - +
228C ALA* 4.2 7.6 - - - -
231C ASP* 2.7 35.1 + - - +
232C GLN* 2.7 23.6 + - - +
326C ARG 4.0 3.8 - - - -
336C ASN* 1.3 75.9 - - - +
338C VAL* 1.3 58.7 + - - +
339C VAL* 3.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LEU* 4.7 2.0 - - + -
213C PHE* 3.6 38.6 - - + -
214C ILE 3.6 3.6 - - - +
215C ILE* 3.5 24.0 - - + -
232C GLN* 2.9 17.6 + - - +
299C TYR* 4.3 13.2 - - + -
326C ARG* 3.0 39.0 + - + +
327C VAL 3.7 5.2 - - - +
328C SER* 3.5 29.2 - - - +
337C SER* 1.3 69.2 + - - +
339C VAL* 1.3 59.8 + - - +
340C ASN 4.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C PHE* 3.3 6.4 - - - -
214C ILE* 2.8 43.9 + - + +
216C LYS* 3.9 22.9 - - + -
231C ASP* 3.8 10.8 - - - +
232C GLN* 4.1 4.0 - - - +
337C SER* 3.8 20.6 - - - +
338C VAL* 1.3 74.3 - - - +
340C ASN* 1.3 72.2 + - - +
341C PRO* 3.3 14.4 - - + +
----------------------------------------------------------
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