Contacts of the strand formed by residues 194 - 201 (chain G) in PDB entry 4XLN
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 LYS 194 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G VAL* 4.5 8.4 - - + +
26G GLU* 3.3 40.9 + - + +
180G GLN 3.6 1.7 - - - +
181G VAL* 3.2 6.2 - - - -
182G GLU* 2.9 76.0 + - + +
183G ASP 4.2 10.1 - - - +
184G THR* 3.6 11.3 - - - +
193G ASP* 1.3 70.8 - - - +
195G LEU* 1.3 61.6 + - - +
196G THR* 3.7 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G PHE 3.2 4.4 - - - +
24G VAL* 3.3 2.4 - - - -
25G LEU* 2.9 51.3 + - + +
28G LEU* 4.2 12.8 - - + -
33G GLY* 3.2 29.6 - - - +
36G LEU* 4.0 12.8 - - + -
37G GLY* 3.5 17.0 - - - +
179G PHE* 4.1 18.4 - - + -
180G GLN 3.9 2.2 - - - +
181G VAL* 4.3 9.2 - - + -
193G ASP 3.8 1.6 + - - -
194G LYS* 1.3 71.4 - - - +
196G THR* 1.3 75.3 + - - +
197G LEU* 3.9 15.7 - - + +
225H PHE* 5.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G GLU* 3.9 18.8 - - - +
23G PHE 3.3 4.5 - - - +
24G VAL* 3.6 26.0 - - + +
178G ALA 3.9 1.0 - - - +
179G PHE* 3.4 1.7 - - - -
180G GLN 2.9 36.3 + - - -
182G GLU* 3.9 15.8 + - - -
194G LYS* 3.9 10.0 + - - -
195G LEU* 1.3 76.7 + - - +
197G LEU* 1.3 61.6 + - - +
198G ARG 3.9 1.1 + - - -
934I PHE* 3.4 33.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G GLU* 3.6 2.4 - - - -
23G PHE* 2.9 49.8 + - + +
37G GLY* 4.2 22.7 - - - +
40G LEU* 4.4 15.3 - - + -
41G ARG 5.3 0.4 - - - +
44G LEU* 4.3 3.8 - - + -
177G VAL* 3.6 29.6 - - + -
178G ALA 4.1 1.8 - - - -
179G PHE* 4.0 13.5 - - + -
195G LEU* 3.9 9.3 - - + +
196G THR* 1.3 72.8 - - - +
198G ARG* 1.3 62.9 + - - +
199G ILE* 3.6 24.5 - - + -
211G LEU* 4.3 20.4 - - + -
225H PHE* 5.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 198 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G TYR* 2.6 22.3 + - + -
21G GLY 3.6 5.2 - - - +
22G GLU* 3.0 20.3 + - - +
176G ARG 3.9 0.7 - - - +
177G VAL* 3.4 7.4 - - - +
178G ALA* 2.9 50.5 + - - +
180G GLN* 6.1 0.4 - - - -
196G THR 4.3 0.4 - - - +
197G LEU* 1.3 74.9 - - - +
199G ILE* 1.3 61.7 + - - +
200G TRP* 3.7 27.5 - - + -
929I ARG* 5.4 3.8 + - - +
932I GLU* 3.1 52.3 + - - +
934I PHE* 3.4 47.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G HIS 3.4 3.8 - - - +
20G TYR* 3.6 2.6 - - - -
21G GLY 2.9 38.8 + - - +
23G PHE* 3.5 20.2 - - + -
44G LEU* 3.6 34.5 - - + -
174G VAL* 4.6 0.2 - - + -
176G ARG 4.1 1.6 - - - -
177G VAL* 4.6 3.4 - - + -
197G LEU* 3.6 21.8 - - + -
198G ARG* 1.3 71.6 - - - +
200G TRP* 1.3 63.4 + - - +
201G THR* 3.6 25.4 - - + -
207G PRO* 3.3 36.3 - - + +
210G ALA* 4.6 0.7 - - + -
211G LEU* 3.7 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 200 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G HIS* 3.6 3.4 - + + -
20G TYR* 3.2 50.6 - + + -
174G VAL* 3.3 3.8 - - - +
175G ARG* 2.4 36.5 + - + -
176G ARG* 2.9 72.1 + - + +
178G ALA* 4.1 7.2 - - + -
198G ARG* 3.7 43.1 - - + -
199G ILE* 1.3 72.0 - - - +
201G THR* 1.3 55.2 + - - +
863I ASP* 4.0 20.9 - - + -
928I LYS* 6.3 0.9 - - - -
932I GLU* 4.1 15.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ASP 2.7 28.8 + - - -
19G HIS* 2.8 27.6 + - - +
173G PRO* 3.2 11.7 - - + -
174G VAL* 3.6 17.5 - - + +
175G ARG* 3.6 9.7 + - - +
199G ILE* 3.6 22.9 - - + -
200G TRP* 1.3 76.7 - - - +
202G ASP* 1.3 61.2 + - - +
203G GLY 3.7 0.4 + - - -
205G VAL 3.1 18.9 + - - +
207G PRO* 3.7 7.3 - - + +
210G ALA* 4.5 6.7 - - + -
----------------------------------------------------------
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