Contacts of the strand formed by residues 148 - 155 (chain 3) in PDB entry 1SVA
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 ASN 148 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1262 LEU* 5.6 1.3 - - - -
1463 GLY 3.8 5.2 + - - +
1473 SER* 1.3 75.1 - - - +
1493 PHE* 1.3 62.1 + - - +
1503 HIS* 4.0 15.1 + - - -
2233 THR 3.8 0.7 - - - +
2243 TYR* 3.5 5.5 - - - -
2253 THR* 2.9 49.7 + - - +
2303 VAL* 5.1 2.3 - - - +
2313 PRO 5.0 1.4 + - - -
2323 PRO* 3.8 24.2 - - - +
2333 VAL 4.8 2.0 + - - +
2663 ILE* 3.0 23.1 - - - +
2673 CYS 3.2 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 149 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222 VAL* 4.3 13.0 - - + -
1232 THR* 3.6 32.1 - - + -
1262 LEU* 4.4 17.9 - - + -
2362 ILE* 4.7 6.1 - - + -
883 TYR* 4.6 6.1 - + - -
1483 ASN* 1.3 77.5 - - - +
1503 HIS* 1.3 63.1 + - - +
1513 PHE* 3.4 35.7 - + + -
2053 VAL* 5.2 0.9 - - + -
2103 PRO* 5.8 2.5 - - + -
2223 GLY 4.5 2.5 - - - -
2233 THR* 3.1 35.4 - - - -
2243 TYR* 3.8 10.5 - + + -
2643 VAL* 3.4 28.3 - - + +
2653 ASP* 3.3 2.6 - - - -
2663 ILE* 2.7 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 150 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193 VAL* 4.9 2.7 - - + +
1483 ASN* 4.0 19.5 + - - -
1493 PHE* 1.3 76.1 - - - +
1513 PHE* 1.3 61.8 + - - +
2223 GLY* 3.1 2.1 - - - -
2233 THR* 3.0 33.6 + - + +
2323 PRO* 5.7 0.6 - - - +
2333 VAL 5.5 2.2 + - - -
2343 LEU* 3.9 27.8 - - + +
2643 VAL 3.1 5.2 - - - -
2653 ASP* 2.7 28.8 + - + +
2663 ILE 3.4 10.3 + - - -
2673 CYS* 3.3 42.8 - - + -
2843 ARG* 5.0 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 151 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2362 ILE* 4.6 4.9 - - + -
883 TYR* 4.1 19.7 - + - -
1493 PHE* 3.4 28.3 - + + -
1503 HIS* 1.3 77.8 - - - +
1523 PHE* 1.3 76.0 + - - +
1533 ALA* 3.7 21.3 - - + -
1593 LEU* 3.8 18.8 - - + -
2103 PRO* 4.1 11.4 - - + -
2203 TYR* 3.4 30.5 - + + -
2213 PHE 3.0 26.0 - - - +
2223 GLY* 3.7 3.1 - - - -
2623 SER 4.4 1.8 - - - -
2633 ALA* 3.2 7.9 - - - +
2643 VAL* 2.7 47.1 + - + +
2653 ASP* 4.3 1.0 + - - -
2843 ARG* 4.3 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1153 VAL* 4.6 14.6 - - + -
1173 THR* 3.7 25.6 - - + -
1513 PHE* 1.3 85.1 - - - +
1533 ALA* 1.3 82.7 + - - +
1543 VAL* 4.3 12.1 - - + -
2203 TYR* 3.2 1.4 - - - +
2213 PHE* 2.8 75.5 + + + +
2423 THR* 5.1 6.1 - - + -
2623 SER 3.3 13.0 - - - +
2633 ALA* 3.7 9.4 - - + -
2843 ARG* 3.8 26.9 - - - -
2863 PHE* 3.7 15.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1513 PHE* 3.7 9.2 - - + -
1523 PHE* 1.3 85.3 - - - +
1543 VAL* 1.3 66.5 + - - +
1593 LEU* 4.6 5.6 - - + -
2183 THR* 4.2 8.1 - - - +
2193 ARG 2.9 16.8 - - - +
2203 TYR* 3.3 15.7 - - + -
2613 VAL* 3.7 2.3 - - - +
2623 SER* 2.9 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123 ALA* 4.3 15.5 - - + -
1153 VAL* 4.5 8.7 - - + -
1523 PHE* 4.3 12.0 - - + -
1533 ALA* 1.3 77.4 - - - +
1553 GLY* 1.3 60.6 + - - +
2183 THR* 3.5 3.1 - - - -
2193 ARG* 2.8 28.7 + - - +
2443 LEU* 4.2 26.9 - - + -
2523 PRO* 3.8 5.1 - - + +
2593 LEU* 4.5 10.1 - - + -
2603 TYR 3.5 6.1 - - - +
2613 VAL* 4.5 3.1 - - + -
2863 PHE* 4.2 23.8 - - + -
2883 ILE* 4.4 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 155 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1543 VAL* 1.3 77.9 - - - +
1563 GLY* 1.3 57.1 + - - -
1573 GLU 3.3 10.6 + - - -
2173 ASN 3.3 12.3 - - - -
2183 THR* 3.4 10.1 - - - -
2523 PRO* 3.6 9.6 - - - -
2593 LEU* 4.0 5.8 - - - +
2603 TYR* 3.0 36.3 + - - +
----------------------------------------------------------
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