Contacts of the strand formed by residues 376 - 382 (chain D) in PDB entry 1UHG
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 376 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D SER* 2.9 13.9 + - - +
8D MET* 3.4 36.8 - - + -
11D CYS* 4.0 15.9 - - + -
12D PHE* 5.2 1.8 - - + -
31D PRO* 4.0 19.3 - - + +
32D ILE* 3.7 24.6 + - - +
264D LEU* 5.1 3.1 - - + -
367D CYS* 3.7 22.7 - - - -
368D ILE 4.0 2.5 - - - -
369D LYS* 4.4 2.7 - - + +
374D ASN 4.8 0.9 - - - +
375D ALA* 1.3 71.9 - - - +
377D LEU* 1.3 61.0 + - - +
378D PHE 3.3 30.3 - - - +
379D PHE* 4.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D CYS* 3.1 29.1 - - - -
31D PRO* 3.2 8.7 - - - +
32D ILE* 3.9 27.9 - - + +
86D ILE* 4.1 22.4 - - + -
90D ILE* 4.3 11.9 - - + -
99D PHE* 5.6 0.4 - - + -
239D MET* 3.6 44.9 - - + -
368D ILE* 2.8 18.1 + - + +
369D LYS 4.2 2.2 - - - -
370D HIS* 4.0 24.0 - - + +
375D ALA* 4.6 1.3 - - + +
376D VAL* 1.3 77.4 - - - +
378D PHE* 1.3 73.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D PHE* 3.5 33.7 - + + -
29D TYR 3.4 6.1 - - - -
30D CYS* 3.6 13.9 - - + -
31D PRO* 3.9 0.9 - - - -
99D PHE* 3.6 28.7 - + - -
178D ILE* 3.1 31.4 - - + -
180D PHE* 3.5 38.4 - + + -
239D MET* 6.3 0.2 - - - -
331D HIS 5.4 0.2 - - - -
366D PHE* 5.7 1.1 - - + -
367D CYS* 3.3 3.9 - - - -
368D ILE* 2.9 53.6 + - + -
376D VAL* 3.3 10.3 - - - +
377D LEU* 1.3 91.1 - - + +
379D PHE* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 379 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D CYS* 3.5 24.0 - - - -
12D PHE* 3.6 29.2 - + - -
15D PHE* 3.7 33.7 - + - -
28D PHE* 3.4 7.0 - - - -
29D TYR* 3.0 60.0 + + + -
31D PRO* 4.2 0.6 - - + +
244D LEU* 5.2 1.6 - - + -
259D ILE* 4.2 8.3 - - + -
365D LEU* 4.0 28.9 - - + -
366D PHE* 3.4 18.2 - - - -
367D CYS* 3.8 16.8 - - + -
376D VAL* 4.3 0.7 - - + -
378D PHE* 1.3 75.4 - - - +
380D GLY* 1.3 72.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 380 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 3.0 15.9 - - - -
28D PHE* 4.1 0.4 - - - -
365D LEU* 3.4 7.4 - - - +
366D PHE* 2.9 49.8 + - - +
379D PHE* 1.3 88.3 - - - +
381D ARG* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 381 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 4.6 4.9 - - + -
19D LYS* 3.9 16.8 + - - +
22D HIS 2.7 28.7 + - - -
23D ALA* 4.7 4.2 - - - +
24D ASN 3.8 7.0 - - - +
25D GLU 2.9 28.4 + - - +
26D ASN* 3.3 9.2 - - - +
27D ILE* 2.9 53.2 + - + +
252D LEU* 3.9 15.8 - - + +
256D GLU* 2.7 39.3 + - - +
287D MET* 3.7 1.4 - - - +
364D PHE 3.6 4.3 - - - +
365D LEU* 3.8 11.2 - - + -
366D PHE* 4.1 1.8 - - - -
380D GLY* 1.3 73.9 - - - -
382D CYS* 1.3 61.5 + - - +
383D VAL* 3.5 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 382 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ASN* 3.6 3.6 - - - -
198D PHE* 4.2 2.4 - - - -
285D MET* 3.9 18.8 - - + -
287D MET* 4.6 4.3 - - + -
363D PRO* 3.2 6.2 - - - +
364D PHE* 2.8 67.8 + - + -
366D PHE* 4.0 3.9 - - + -
381D ARG* 1.3 73.9 - - - +
383D VAL* 1.3 59.5 + - - +
384D SER 4.1 2.2 - - - -
385D PRO* 3.7 43.5 - - - -
----------------------------------------------------------
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