Contacts of the strand formed by residues 119 - 125 (chain G) in PDB entry 3WUW
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 119 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G ALA* 4.1 2.5 - - + -
108G HIS 3.4 16.8 - - - +
109G PRO* 4.5 2.0 - - + -
110G GLY 3.4 25.6 - - - +
111G PRO* 5.5 0.2 - - + -
113G VAL* 3.7 23.6 - - + -
118G ARG* 1.3 76.0 - - - +
120G ILE* 1.3 76.6 + - - +
121G LEU* 3.9 16.8 - - + -
159G PHE 3.8 0.2 - - - +
160G SER* 3.7 3.3 + - - -
161G ILE* 2.9 55.4 + - + +
164G MET* 5.2 0.7 - - - -
194G ILE* 4.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G LEU 3.7 0.7 - - - +
107G ALA* 3.3 5.2 - - - -
108G HIS* 2.8 52.1 + - + +
118G ARG* 6.2 0.9 - - + -
119G VAL* 1.3 79.3 - - - +
121G LEU* 1.3 70.5 + - - +
122G GLN 4.3 1.1 - - - +
158G ASN* 3.7 39.7 - - + +
159G PHE 3.4 5.4 - - - +
160G SER* 4.0 24.5 - - - +
301G NAG 4.3 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G LEU* 4.0 15.5 - - + -
106G LEU 3.6 2.5 - - - -
107G ALA* 3.9 15.9 - - + -
119G VAL* 3.9 22.2 + - + -
120G ILE* 1.3 80.8 - - - +
122G GLN* 1.3 60.9 + - - +
134G LEU* 3.9 20.6 - - + -
159G PHE* 2.8 44.7 + - - +
161G ILE* 4.3 7.9 - - + -
172G TYR* 3.7 44.9 - - + -
192G LEU* 4.7 4.3 - - + -
194G ILE* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G SER 3.5 1.0 - - - +
105G LEU* 3.3 6.5 - - - -
106G LEU* 2.9 47.3 + - + +
108G HIS* 3.0 35.1 + - + +
120G ILE* 3.8 1.0 + - + -
121G LEU* 1.3 72.9 - - - +
123G CYS* 1.3 68.8 + - - +
124G TRP* 4.5 9.4 - - + -
156G LYS* 3.8 27.7 - - - +
157G ALA 3.4 6.7 - - - +
158G ASN* 3.5 23.7 + - - +
301G NAG 3.9 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 123 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G PRO* 3.7 12.6 - - - -
104G SER 3.2 3.6 - - - -
105G LEU* 4.7 0.9 - - + -
121G LEU 3.8 1.4 + - - -
122G GLN* 1.3 74.6 - - - +
124G TRP* 1.3 61.9 + - - +
132G PHE* 3.3 38.1 - - + -
156G LYS* 3.1 4.2 - - - +
157G ALA 2.9 34.4 + - - +
159G PHE* 4.4 7.2 - - + -
174G CYS* 2.1 52.0 - - + -
175G TYR 4.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G PRO* 3.5 2.4 - - - +
104G SER* 2.9 62.6 + - - -
106G LEU* 3.3 34.6 - - + +
122G GLN* 4.3 9.6 - - + -
123G CYS* 1.3 78.2 - - - +
125G SER* 1.3 73.7 - - - +
126G ASP* 4.3 18.6 - - - -
132G PHE* 4.1 2.2 - - - -
154G VAL* 4.6 18.4 - - + -
155G SER 3.3 12.3 - - - +
156G LYS* 3.7 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G LYS 4.7 2.8 + - - -
103G PRO* 4.1 10.4 - - - +
124G TRP* 1.3 88.4 - - - +
126G ASP* 1.3 60.7 + - - +
127G ILE* 3.0 26.0 + - - +
129G PHE* 3.3 33.5 - - - -
132G PHE* 4.5 2.0 - - - -
154G VAL* 3.3 4.1 - - - -
155G SER 2.9 31.0 + - - -
----------------------------------------------------------
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