Contacts of the strand formed by residues 212 - 224 (chain R) in PDB entry 4V1N
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 THR 212 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139Q LEU* 5.0 14.8 - - - -
58R ASP 3.6 19.7 + - - +
59R LEU* 3.9 4.9 - - - -
60R ASP* 3.3 18.3 + - - +
135R PHE* 5.8 3.8 - - - -
136R THR 3.3 7.2 - - - -
137R GLU* 4.7 3.4 - - - +
210R LYS 3.6 3.0 + - - -
211R LYS* 1.3 77.9 - - - +
213R ALA* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59R LEU* 5.6 0.9 - - - -
60R ASP* 3.1 20.9 - - + +
135R PHE* 3.0 8.8 - - - +
136R THR* 2.8 38.2 + - - +
211R LYS* 4.2 0.6 + - + +
212R THR* 1.3 74.9 - - - +
214R ILE* 1.3 61.0 + - - +
215R VAL* 3.4 5.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59R LEU* 4.9 6.3 - - + -
60R ASP* 3.0 27.8 + - - +
61R LEU 3.7 4.2 + - - -
62R GLU* 3.1 35.5 + - + +
133R TYR* 6.3 2.5 - - + -
134R VAL 3.7 6.5 - - - -
135R PHE* 4.4 5.4 - - + +
213R ALA* 1.3 70.4 - - - +
215R VAL* 1.4 63.0 + - - +
216R GLY 3.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R GLU* 5.1 2.7 - - - -
66R ARG* 3.7 16.6 + - - +
134R VAL* 2.9 23.6 + - + +
135R PHE* 5.1 0.9 - - - -
136R THR* 5.2 8.1 - - - +
213R ALA* 3.4 8.3 + - + +
214R ILE* 1.4 73.8 - - - +
216R GLY* 1.3 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R GLU* 5.5 9.5 - - - +
66R ARG* 3.2 17.5 - - - -
67R GLN* 5.3 2.0 - - - -
68R VAL* 5.4 6.1 - - - -
133R TYR* 3.5 6.1 - - - +
134R VAL* 2.9 29.5 + - - +
214R ILE 3.7 2.0 - - - -
215R VAL* 1.3 81.8 - - - +
217R THR* 1.3 60.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 217 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R GLU* 6.5 0.4 - - - -
65R ASN* 6.1 2.7 - - - -
66R ARG 2.9 9.9 + - - -
67R GLN* 3.5 4.6 - - - -
68R VAL* 3.0 23.6 + - - -
132R GLU 3.6 9.4 - - - -
133R TYR* 4.3 3.1 - - - +
216R GLY* 1.3 74.3 - - - -
218R VAL* 1.3 63.5 + - - +
219R CYS* 3.2 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R VAL* 3.5 11.4 - - - +
69R TRP 5.4 0.4 - - - -
70R LEU* 4.8 14.6 - - + +
127R LYS* 5.3 8.0 - - - +
132R GLU* 2.9 38.9 + - + +
133R TYR* 4.7 1.0 - - - +
217R THR* 1.3 72.3 - - - +
219R CYS* 1.3 60.5 - - - +
220R HIS 3.5 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 219 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67R GLN* 3.7 26.7 - - + -
68R VAL 3.0 8.6 + - - +
127R LYS* 5.5 6.2 - - - +
217R THR* 3.2 4.0 + - - -
218R VAL* 1.3 73.0 - - - +
220R HIS* 1.4 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 220 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R VAL 3.8 2.9 + - - +
69R TRP* 3.4 13.9 - - + +
70R LEU* 3.1 24.8 + - - +
125R THR 5.3 1.6 - - - +
127R LYS* 6.4 0.7 - - - +
218R VAL* 3.5 4.4 - - - +
219R CYS* 1.4 83.0 + - + +
221R GLU* 1.3 63.6 + - - +
222R CYS* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R LEU* 3.4 12.6 - - + +
124R LEU* 3.9 3.5 - - - +
125R THR* 3.0 43.5 + - - +
126R LYS 4.2 14.5 - - - +
127R LYS* 5.3 3.9 - - - +
220R HIS* 1.3 78.6 - - - +
222R CYS* 1.3 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 222 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R TRP* 6.2 2.9 - - + -
70R LEU 3.0 9.2 + - - +
71R VAL* 3.3 12.4 - - + -
72R ARG* 3.0 22.5 + - - +
122R LEU* 4.7 13.9 - - + -
123R GLU 3.5 10.1 - - - +
124R LEU* 4.8 3.8 - - + -
125R THR* 4.5 2.7 - - - +
220R HIS* 6.2 0.9 - - + -
221R GLU* 1.3 77.9 - - - +
223R GLN* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 223 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R ARG* 3.8 15.9 - - + +
122R LEU* 3.1 5.8 - - - -
123R GLU* 2.8 42.7 + - + +
125R THR* 6.5 0.4 - - - -
222R CYS* 1.3 75.5 - - - +
224R VAL* 1.3 64.3 + - - +
225R MET* 3.5 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R VAL* 5.5 4.8 - - + +
72R ARG 2.8 22.5 + - - +
73R LEU* 4.5 10.0 - - + -
74R PRO* 4.4 12.4 - - - +
106R LEU* 5.4 8.5 - - + -
120R TYR* 4.9 9.4 - - + +
121R ASP 3.8 5.4 - - - +
122R LEU* 4.4 5.8 - - + +
223R GLN* 1.3 74.0 - - - +
225R MET* 1.3 63.5 + - - +
226R PRO 3.8 0.9 - - - -
----------------------------------------------------------
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