Contacts of the strand formed by residues 123 - 130 (chain B) in PDB entry 5DIR
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 123 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 3.4 35.5 - - + +
30B PHE* 5.7 0.2 - - + -
31B GLN* 3.4 34.8 - - + +
51B LEU* 3.9 25.4 - - + -
52B ALA 3.7 3.1 - - - +
53B TYR* 4.2 9.4 - - + -
115B ASP* 3.5 9.5 + - - +
119B LEU* 3.8 18.4 - - + -
121B HIS* 4.6 0.4 - - - +
122B VAL* 1.3 74.5 - - - +
124B ASP* 1.3 59.7 + - - +
125B PHE* 4.4 3.1 - - + -
140B ASN* 2.7 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 4.2 0.3 - - - +
51B LEU* 3.6 3.6 + - - +
52B ALA* 2.7 47.2 + - + +
54B ASN* 4.1 0.9 - - - -
55B THR 2.8 26.0 + - - -
122B VAL* 3.5 3.9 - - - +
123B VAL* 1.3 84.7 - - - +
125B PHE* 1.3 59.8 + - - +
126B ILE 4.0 0.2 - - - -
138B ALA* 3.1 35.9 - - + +
139B PHE* 3.7 4.6 - - - -
140B ASN* 3.0 10.2 + - - -
143B ASP* 3.7 0.7 - - - +
203H SER* 2.9 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP 4.9 0.2 - - - -
26B SER* 3.4 32.8 - - - -
27B LYS* 3.9 21.3 - - + -
30B PHE* 3.4 44.4 - + + -
49B TRP* 3.4 16.8 - + - -
50B THR* 2.8 46.7 + - - +
51B LEU* 5.3 0.9 - - + -
123B VAL* 4.4 2.5 - - + -
124B ASP* 1.3 76.7 - - - +
126B ILE* 1.3 82.4 + - + +
139B PHE 3.0 2.6 + - - -
140B ASN* 3.5 26.0 - - + -
141B LEU* 3.9 13.5 - - + -
207B OLC 4.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 3.5 28.0 - - + -
48B SER 4.4 0.9 - - - -
49B TRP* 4.1 9.6 - - + -
124B ASP 4.0 0.2 - - - -
125B PHE* 1.3 98.7 - - + +
127B LEU* 1.3 56.9 + - - +
128B VAL* 3.8 3.3 + - + -
138B ALA* 3.3 6.1 - - - -
139B PHE* 2.9 66.7 + - + +
140B ASN 3.9 26.9 - - - -
141B LEU* 4.3 10.1 - - + +
144B SER* 4.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN* 3.4 35.9 - - + +
46B LEU 3.8 0.2 - - - +
47B PHE* 3.5 3.8 - - - -
48B SER* 2.9 56.5 + - - +
50B THR* 3.8 17.0 - - + +
125B PHE 3.6 0.8 + - - -
126B ILE* 1.3 72.8 - - - +
128B VAL* 1.3 61.7 + - - +
129B HIS* 3.9 2.5 - - + -
135B TYR* 4.1 28.9 - - + -
136B PHE 3.8 20.0 - - - +
138B ALA* 4.3 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.3 12.1 - - + +
47B PHE* 4.4 16.6 - - + -
126B ILE* 3.8 4.8 + - + -
127B LEU* 1.3 74.7 - - - +
129B HIS* 1.3 70.3 + - - +
134B TRP* 4.6 13.9 - - + -
135B TYR* 3.8 1.0 - - - +
136B PHE* 2.9 38.7 + - + +
139B PHE* 3.9 30.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 6.2 1.0 - - - +
43B ILE 4.3 1.4 + - - -
44B PRO* 3.2 26.8 + - - +
45B ASP 3.1 16.0 - - - +
46B LEU* 2.8 43.8 + - - +
47B PHE* 3.9 3.5 + - - -
48B SER* 4.4 12.3 + - - -
127B LEU* 3.9 12.3 - - + -
128B VAL* 1.3 78.4 - - - +
130B TRP* 1.3 61.4 + - - +
131B GLN* 2.9 33.2 + - - -
134B TRP* 3.3 26.3 - - - +
135B TYR* 3.4 31.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 3.4 30.3 - - + -
46B LEU* 3.6 22.0 - - + -
129B HIS* 1.3 74.0 - - - +
131B GLN* 1.3 98.6 + - - +
133B ARG* 3.0 35.5 + - + +
134B TRP* 3.0 34.9 + - + +
206B OLC 3.1 60.2 + - + +
----------------------------------------------------------
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