Contacts of the strand formed by residues 93 - 102 (chain D) in PDB entry 6VVT
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 GLY 93 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ILE 4.9 0.5 - - - +
23D TRP* 5.9 0.3 - - - +
24D SER* 2.9 18.9 - - - -
25D TYR 5.5 0.2 - - - -
26D GLY 3.6 9.0 - - - -
28D VAL* 5.3 0.4 - - - -
51D ILE* 5.7 0.9 - - - -
52D PHE* 3.8 13.2 - - - -
92D MET* 1.3 77.6 - - - +
94D HIS* 1.3 60.8 + - - +
318D PRO* 3.4 5.4 - - - +
319D VAL* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ILE* 4.0 15.5 - - + +
21D ARG* 4.5 15.1 - - + +
24D SER* 2.8 32.1 + - - -
26D GLY 3.7 2.0 + - - -
27D GLU* 3.3 37.1 - - + +
28D VAL* 3.2 26.6 + - - +
93D GLY* 1.3 75.3 - - - +
95D ILE* 1.3 66.4 + - - +
96D GLU* 3.6 34.7 + - + +
316D ALA* 4.1 10.1 - - + -
317D VAL 3.0 13.9 - - - +
319D VAL* 3.6 3.7 - - - +
57J ARG 3.7 15.5 - - - -
58J ASN* 4.1 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLU* 4.3 4.0 - - - +
28D VAL* 3.7 14.1 - - + +
46D LEU* 6.0 0.7 - - + -
94D HIS* 1.3 83.9 - - - +
96D GLU* 1.3 61.3 + - - +
97D LEU* 3.4 12.0 + - + +
316D ALA* 3.1 4.5 - - - -
317D VAL* 2.7 41.1 + - + +
319D VAL* 3.5 21.8 - - + -
344D TYR* 4.0 20.0 - - + +
347D VAL* 4.4 19.5 - - + -
348D ILE* 4.3 26.9 - - + -
351D ASN* 3.7 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ARG* 2.2 51.7 + - - +
27D GLU* 3.3 26.9 + - - +
94D HIS* 3.6 16.6 + - - +
95D ILE* 1.3 70.3 - - - +
97D LEU* 1.3 63.9 + - - +
98D ALA 3.7 0.3 + - - -
315D ASP* 3.3 14.1 - - - +
316D ALA* 3.7 6.7 - - - +
351D ASN* 2.9 20.1 + - - -
355D LYS* 4.3 7.7 - - - +
58J ASN 5.0 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ILE* 3.9 25.6 - - + +
96D GLU* 1.3 74.4 - - - +
98D ALA* 1.3 62.1 + - - +
99D ALA* 3.1 19.8 + - - +
101D VAL* 4.0 23.1 - - + -
314D LEU* 3.5 22.9 - - + +
315D ASP* 2.9 22.4 + - - +
317D VAL* 3.7 27.6 - - + -
347D VAL* 4.7 5.6 - - + -
351D ASN* 3.6 4.5 - - - +
374D LEU* 4.3 22.2 - - + -
378D VAL* 4.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLU 3.7 1.4 + - - -
97D LEU* 1.3 70.6 - - - +
99D ALA* 1.3 59.8 + - - +
100D PRO* 4.9 0.2 - - - +
351D ASN* 2.8 20.0 + - - +
354D LEU* 3.7 22.0 - - + +
355D LYS* 3.9 29.1 - - + +
358D ILE* 5.4 5.4 - - + +
371D LYS* 5.1 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU* 3.1 20.3 - - - +
98D ALA* 1.3 82.0 - - - +
100D PRO* 1.3 80.6 - - + +
259D GLU* 5.7 2.0 - - - +
354D LEU* 3.7 19.6 - - + +
371D LYS* 4.1 28.5 - - + +
374D LEU* 3.7 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU 5.7 0.2 - - - +
98D ALA 4.9 0.2 - - - +
99D ALA* 1.3 94.6 - - + +
101D VAL* 1.3 63.3 + - - +
258D ALA* 3.3 16.2 + - + +
259D GLU* 3.9 47.1 + - + +
262D LYS* 4.0 20.9 - - + +
313D VAL* 4.9 5.4 - - + -
314D LEU 3.6 9.6 - - - +
315D ASP* 3.6 22.4 - - - +
371D LYS* 6.0 0.7 - - - +
375D GLN* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU* 4.0 14.4 - - + -
99D ALA 4.0 5.8 - - - +
100D PRO* 1.3 80.8 - - - +
102D THR* 1.3 77.4 + - - +
258D ALA* 3.6 5.2 - - - -
313D VAL* 3.3 2.9 - - - -
314D LEU* 2.7 40.4 + - + +
371D LYS 5.1 0.9 - - - +
374D LEU* 4.0 19.7 - - + +
375D GLN* 3.3 36.6 - - + +
378D VAL* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D VAL* 1.3 81.3 - - - +
103D HIS* 1.3 65.3 + - - +
104D ILE* 3.3 2.9 + - - -
107D PHE* 4.6 7.6 - - + +
114D LEU* 4.9 7.0 - - + -
129D ILE* 3.1 44.9 - - + +
258D ALA* 3.7 17.5 - - + -
261D ILE* 4.8 5.6 - - + -
312D MET 3.7 6.5 - - - -
313D VAL* 4.1 12.6 - - + +
314D LEU* 4.1 0.2 - - - -
375D GLN* 2.7 40.2 + - - -
378D VAL* 5.0 1.6 - - - +
379D ASP* 3.6 2.1 - - - +
----------------------------------------------------------
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