Contacts of the strand formed by residues 8 - 13 (chain L) in PDB entry 6XAV
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 ARG 8 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L LYS* 2.9 51.6 + - - +
7L LYS* 1.3 74.8 - - - +
9L TRP* 1.3 67.4 + - - +
10L TYR* 3.7 27.5 + - + +
71L VAL 3.4 0.5 - - - +
72L GLN* 3.2 3.6 - - - -
73L MET 2.7 41.4 + - - +
74L VAL* 4.1 13.5 - - - +
75L MET 5.8 0.7 - - - +
102L PRO* 6.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 9 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L LYS* 5.8 1.1 - - - -
7L LYS 4.8 4.0 + - - -
8L ARG* 1.3 79.7 - - - +
10L TYR* 1.3 75.5 + - - +
41L GLU* 3.9 12.3 - - + -
43L MET* 3.9 16.8 - - + -
70L LEU* 3.6 42.6 - - + -
71L VAL 3.3 17.5 - - - -
72L GLN* 3.8 39.6 - - + +
102L PRO* 4.2 2.8 - - - +
103L ILE* 3.4 35.4 + - + +
104L SER 5.5 0.2 - - - +
108L VAL* 3.5 36.0 - - + +
112L MET* 6.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 10 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L ARG* 3.7 31.1 - - + +
9L TRP* 1.3 77.6 - - - +
11L VAL* 1.3 66.9 + - - +
70L LEU* 3.3 9.1 - - - +
71L VAL* 2.9 41.2 + - + -
73L MET* 3.6 34.1 - - + -
75L MET* 3.5 33.3 + - + +
92L PHE* 4.3 15.5 - + + -
100L PRO* 4.7 15.0 - - + -
101L ALA 4.0 9.6 - - - -
102L PRO* 3.8 35.4 - - + +
103L ILE* 4.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290J ILE* 3.7 39.9 - - + +
291J ILE* 3.9 9.0 - - + -
10L TYR* 1.3 80.6 - - - +
12L VAL* 1.3 70.2 + - - +
13L GLN* 3.7 15.4 + - + +
68L TYR* 4.1 25.8 - - + -
69L VAL 3.3 9.0 - - - +
70L LEU* 3.7 16.4 - - + -
92L PHE* 3.1 23.1 - - - +
93L ILE 4.7 1.9 + - - -
101L ALA 5.7 1.2 + - - -
103L ILE* 5.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L VAL* 1.3 70.7 - - - +
13L GLN* 1.3 60.2 + - - +
14L ALA 4.2 0.4 + - - -
22L VAL* 5.1 10.3 - - + +
26L LEU* 4.5 18.6 - - + -
42L VAL* 6.1 0.2 - - + -
67L GLY 4.0 4.0 - - - +
69L VAL* 3.0 38.1 + - + +
71L VAL* 3.6 28.5 - - + -
83L VAL* 3.6 33.4 - - + +
86L VAL* 5.5 1.3 - - + -
89L VAL* 3.8 23.1 - - + -
91L GLY* 4.7 2.9 - - - +
92L PHE* 3.7 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 13 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294J ASN* 2.9 49.2 + - - +
297J ARG* 3.8 6.3 - - - +
298J MET* 4.4 10.7 - - - +
11L VAL* 3.7 16.0 + - + +
12L VAL* 1.3 75.2 - - - +
14L ALA* 1.3 74.3 + - - +
67L GLY 4.4 3.6 - - - +
68L TYR* 3.8 19.6 - - + -
89L VAL* 4.2 4.0 - - - -
90L MET* 3.4 10.7 - - - +
91L GLY 2.9 37.9 + - - +
93L ILE* 3.4 24.4 - - + +
----------------------------------------------------------
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