Contacts of the strand formed by residues 98 - 106 (chain D) in PDB entry 2W8B
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 ALA 98 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ARG* 4.3 9.2 - - - +
36D PRO 5.2 0.8 + - - -
37D ILE* 3.3 9.9 - - + +
38D GLY 3.0 22.3 + - - -
96D ILE* 3.1 7.3 - - - +
97D ASP* 1.3 88.1 + - - +
99D VAL* 1.3 64.8 + - - +
118D LEU* 3.9 19.1 - - + -
119D VAL 3.3 10.5 - - - +
121D THR* 3.2 1.5 + - - -
129D LEU* 4.6 9.0 - - + -
156D LEU* 4.4 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLY* 3.2 7.0 - - - +
40D VAL* 3.7 28.3 - - + -
80D PRO* 4.9 0.2 - - + -
86D VAL* 4.5 9.4 - - + -
91D TRP* 3.3 48.7 - - + -
98D ALA* 1.3 81.2 - - - +
100D VAL* 1.3 67.4 + - - +
101D VAL* 3.9 11.3 + - + -
117D GLN 3.7 0.7 - - - +
118D LEU* 3.6 1.7 - - - -
119D VAL* 2.8 40.9 + - + +
121D THR* 3.6 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 4.4 4.5 - - + -
38D GLY 2.8 17.1 + - - +
39D VAL* 4.1 21.3 - - + -
40D VAL* 3.1 26.2 + - - +
42D PHE* 4.0 20.6 - - + -
58D VAL* 4.5 11.0 - - + -
62D LEU* 4.9 0.2 - - + -
99D VAL* 1.3 75.5 - - - +
101D VAL* 1.3 76.1 + - - +
116D TYR* 4.3 12.6 - - + -
117D GLN 3.4 6.5 - - - +
118D LEU* 4.1 16.6 - - + -
148D ALA* 6.2 0.2 - - + -
152D VAL* 4.2 20.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
40D VAL* 4.2 7.4 - - + -
42D PHE* 4.0 7.0 - - - -
80D PRO* 3.6 31.6 - - + +
82D SER* 3.8 24.0 - - - +
83D ALA* 3.9 5.4 - - - +
86D VAL* 3.9 22.2 - - + -
99D VAL* 3.9 6.9 + - + +
100D VAL* 1.3 80.0 - - - +
102D GLY* 1.3 60.2 + - - +
116D TYR* 3.2 6.8 - - - +
117D GLN* 2.8 55.3 + - + +
119D VAL* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PRO 4.7 0.8 + - - +
42D PHE* 3.2 21.7 - - - +
43D GLN* 2.8 22.9 + - - +
80D PRO 5.4 0.2 + - - -
81D GLY* 4.1 3.1 + - - +
101D VAL* 1.3 79.4 - - - +
103D GLN* 1.3 78.5 + - - +
115D ALA 3.1 13.7 - - - -
116D TYR* 3.9 0.9 - - - -
117D GLN* 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 3.6 1.6 - - - -
43D GLN* 3.4 15.7 - - + +
81D GLY 3.1 27.1 + - - +
82D SER* 4.1 4.9 - - - +
102D GLY* 1.3 83.2 - - - +
104D VAL* 1.3 64.4 + - - +
105D THR* 4.2 12.8 - - + -
113D ASN 3.6 2.4 - - - +
114D VAL* 3.6 1.6 - - - -
115D ALA* 2.9 44.0 + - + +
117D GLN* 2.9 42.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 4.0 17.0 - - + -
43D GLN 2.7 12.7 + - - +
44D TRP* 3.3 26.0 - - + -
45D ALA 3.1 25.1 + - - -
50D ALA* 5.8 2.7 - - + -
51D PRO* 4.8 9.9 - - + -
52D GLU 5.3 4.9 - - - +
54D ILE* 3.8 28.5 - - + +
103D GLN* 1.3 76.6 - - - +
105D THR* 1.3 63.9 + - - +
112D TYR* 4.5 13.5 - - + -
113D ASN 3.2 9.6 - - - +
114D VAL* 4.6 10.8 - - + -
141D LEU* 5.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ALA* 3.8 15.9 - - + -
103D GLN* 4.8 11.0 - - + -
104D VAL* 1.3 83.8 - - - +
106D PRO* 1.3 70.2 - - - +
112D TYR* 3.3 9.8 - - - +
113D ASN* 2.8 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D TRP* 4.0 23.8 - - + -
45D ALA* 3.8 27.8 - - + +
46D GLY* 5.5 0.7 - - - -
105D THR* 1.3 89.9 - - - +
107D ASN* 1.3 65.7 - - - +
108D PRO* 4.6 1.6 - - - +
111D SER 3.8 5.4 - - - +
112D TYR* 4.0 9.6 - - + -
113D ASN* 4.7 0.2 - - - +
----------------------------------------------------------
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