Contacts of the strand formed by residues 108 - 115 (chain I) in PDB entry 6XXD
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 108 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 5.6 1.3 - - - -
21F ILE* 4.2 20.9 - - - -
22F PRO 5.4 1.3 + - - -
24F LEU* 6.2 1.1 - - - -
44I VAL* 5.6 2.7 - - - -
103I ALA* 3.5 0.8 - - - -
104I THR 2.9 35.3 + - - -
105I PRO 3.9 4.5 + - - -
106I ASP 3.5 2.4 - - - -
107I LYS* 1.3 80.9 - - - +
109I VAL* 1.3 61.3 + - - -
110I TYR* 3.4 10.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F ALA* 4.7 8.7 + - + +
18F ALA* 4.6 18.0 - - - +
21F ILE* 4.9 8.9 - - + +
37I THR* 4.3 24.9 - - + +
40I LEU* 3.8 37.2 - - + +
41I ASN* 4.0 11.0 - - + +
44I VAL* 3.9 27.4 - - + -
101I PHE* 4.8 4.0 - - + -
102I ALA 3.6 13.0 - - - +
103I ALA* 4.1 3.4 - - + +
107I LYS 4.8 1.3 - - - +
108I GLY* 1.3 71.4 - - - -
110I TYR* 1.3 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 110 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I PHE* 3.4 9.7 - - - +
102I ALA* 2.8 52.1 + - + +
104I THR* 4.2 8.7 - - + +
107I LYS* 3.5 52.2 - - + +
108I GLY 3.4 15.7 - - - -
109I VAL* 1.3 73.5 - - - +
111I LYS* 1.3 69.4 + - - +
124I CYS* 3.7 7.6 - - - +
125I PRO* 2.7 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ARG* 5.2 3.0 - - - +
98I THR* 5.7 0.9 - - - +
99I VAL* 4.0 23.1 - - + +
100I TRP 3.7 4.3 - - - +
101I PHE* 3.7 28.0 - - + -
110I TYR* 1.3 86.3 - - - +
112I THR* 1.3 61.9 + - - +
113I ASN* 5.1 1.6 - - - +
52L ILE* 3.7 28.4 + - - +
53L ASP* 3.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 112 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I ILE* 6.0 1.8 - - + -
99I VAL* 3.4 23.4 - - - +
100I TRP* 3.0 41.1 + - + +
101I PHE* 4.8 1.1 - - - +
102I ALA* 5.3 4.5 - - + +
110I TYR* 4.2 3.0 + - - -
111I LYS* 1.3 75.0 - - - +
113I ASN* 1.3 74.0 + - - +
114I THR* 3.8 20.6 + - - +
121I PRO* 4.2 9.0 - - + +
125I PRO* 3.6 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 113 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I VAL* 4.2 7.0 - - - +
111I LYS 5.1 1.2 - - - +
112I THR* 1.3 82.8 + - - +
114I THR* 1.3 61.1 + - - +
115I ALA* 3.5 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I VAL* 3.3 7.9 - - - +
100I TRP* 3.2 29.1 + - + +
112I THR* 3.3 10.1 + - - +
113I ASN* 1.3 76.4 - - - +
115I ALA* 1.3 68.2 + - - +
118I SER* 4.2 8.5 - - - -
119I SER 3.5 25.1 - - - +
121I PRO* 3.8 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I THR 4.0 12.1 - - - +
99I VAL* 4.2 2.9 - - + -
100I TRP* 2.9 16.7 + - - -
113I ASN 3.5 3.5 + - - +
114I THR* 1.3 75.5 - - - +
116I VAL* 1.3 64.0 - - + +
117I THR* 3.3 18.2 - - + +
118I SER* 3.2 24.3 + - - +
----------------------------------------------------------
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