Contacts of the strand formed by residues 123 - 131 (chain B) in PDB entry 6DU3
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
----------------------------------------------------------
143A GLY 6.1 0.7 - - - +
169A TRP 3.4 28.5 - - - +
170A GLY* 4.0 15.7 - - - +
173A ARG* 4.5 11.0 - - - +
118B VAL 3.6 0.2 - - - +
119B GLU* 3.1 1.4 - - - -
120B ILE 2.7 39.3 + - - +
121B ASP 2.7 16.0 + - - +
122B GLY* 1.3 75.2 - - - +
124B VAL* 1.3 71.6 + - - +
125B HIS* 3.7 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLU* 4.6 14.9 - - - +
117B PRO* 3.6 32.8 - - + -
118B VAL 3.5 7.9 - - - +
119B GLU* 4.1 13.7 - - + +
122B GLY 4.7 5.6 - - - +
123B VAL* 1.3 80.6 - - - +
125B HIS* 1.3 65.2 + - - +
126B GLN* 5.6 1.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN* 3.2 40.4 - - + +
90A LYS* 4.3 7.2 - - - +
143A GLY 5.3 0.4 - - - -
144A GLU* 5.8 3.1 - - - +
173A ARG* 2.9 35.8 + - - -
106B PHE* 3.3 26.5 - + + -
117B PRO* 3.3 6.1 - - - +
118B VAL 2.7 33.6 + - - +
120B ILE* 3.8 24.7 - - + +
123B VAL* 3.8 28.2 + - + +
124B VAL* 1.3 76.0 - - - +
126B GLN* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LYS* 6.2 0.4 - - - +
141A ARG* 3.3 24.6 + - - +
144A GLU* 3.5 40.1 + - + +
145A LEU* 5.8 0.3 - - - +
106B PHE* 3.4 24.9 - - - +
115B ILE* 4.0 26.0 - - + +
116B ILE 3.9 2.9 - - - +
117B PRO* 5.2 6.3 - - + -
124B VAL* 5.6 1.3 - - + +
125B HIS* 1.3 77.4 - - - +
127B VAL* 1.3 63.7 + - - +
128B TYR* 4.0 22.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B SER* 3.7 18.8 - - - -
105B SER 3.7 8.1 - - - +
106B PHE* 3.4 36.6 - - + -
114B PHE 3.7 0.3 - - - +
115B ILE* 3.3 6.1 - - - -
116B ILE* 2.9 43.6 + - + +
118B VAL* 3.8 20.6 - - + -
126B GLN* 1.3 72.5 - - - +
128B TYR* 1.3 65.0 + - - +
129B VAL* 3.9 2.0 + - + -
158B TYR* 3.6 25.1 - - + -
860D LEU* 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 4.3 10.0 + - - -
145A LEU* 4.9 0.7 - - - +
246A ARG* 4.3 10.1 + - - -
103B HIS 3.9 1.0 - - - +
104B SER* 3.1 23.2 - - - -
105B SER* 2.9 17.2 + - - +
106B PHE 4.5 1.6 - - - -
107B LYS 3.7 18.8 - - - +
108B PRO* 3.6 28.2 - - + +
109B VAL* 3.3 38.1 - - + -
112B ALA* 3.6 19.5 - - + -
114B PHE 3.6 2.2 - - - -
115B ILE* 3.8 28.9 - - + +
126B GLN* 4.0 33.9 + - + -
127B VAL* 1.3 75.2 - - - +
129B VAL* 1.3 59.7 + - - +
130B LEU* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL* 3.7 27.4 - - + -
104B SER* 3.2 23.8 - - - +
112B ALA* 4.1 1.1 - - - +
113B ASP* 2.8 32.4 + - - +
114B PHE* 2.8 47.7 + - + +
116B ILE* 4.3 8.5 - - + -
127B VAL* 4.1 13.0 - - + -
128B TYR* 1.3 74.6 - - - +
130B LEU* 1.3 58.3 + - - +
162B VAL* 4.1 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL* 3.1 10.2 - - - +
103B HIS* 2.9 42.5 + - + +
109B VAL* 4.8 11.4 - - + -
111B ASN* 3.4 46.7 - - - +
112B ALA* 3.9 8.3 - - - -
113B ASP* 3.9 3.8 - - - +
128B TYR 5.6 1.1 - - - +
129B VAL* 1.3 73.5 - - - +
131B LYS* 1.3 62.5 + - - +
225B TRP* 3.9 13.5 - - + -
226B PHE 3.9 17.3 - - - +
227B ASP* 4.4 15.9 - - + -
229B MET* 5.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU 4.2 3.4 - - - -
102B VAL* 4.4 5.8 - - + -
113B ASP* 2.7 41.6 + - + +
114B PHE* 4.0 27.4 - - + -
130B LEU* 1.3 73.1 - - - +
132B ARG* 1.3 64.3 + - - +
133B PRO 3.7 1.2 - - - -
135B VAL* 3.7 22.2 - - + -
136B ASP* 2.7 35.0 + - - -
166B LEU* 4.7 7.5 + - + +
168B LYS* 4.6 6.1 - - - +
225B TRP* 3.2 12.9 - - - -
229B MET* 3.9 12.1 - - - +
----------------------------------------------------------
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