Contacts of the strand formed by residues 405 - 411 (chain 2) in PDB entry 5IY8
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 GLU 405 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91 LEU* 3.1 27.8 - - - +
101 ILE* 3.4 26.4 + - + +
4042 THR* 1.3 79.5 - - - +
4062 GLY* 1.3 80.1 + - - +
4072 VAL* 3.7 2.8 - - + +
4312 LEU* 5.5 1.6 - - - +
4332 PHE* 4.1 19.4 - - + -
4452 PRO* 3.5 41.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 406 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91 LEU* 3.9 16.0 - - - +
4052 GLU* 1.3 83.3 + - - +
4072 VAL* 1.3 59.3 + - - -
4452 PRO* 3.3 5.5 - - - +
4462 ALA* 2.8 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 407 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 GLY* 3.3 3.6 - - - -
81 VAL* 2.4 65.0 + - + +
91 LEU* 4.0 0.8 - - - +
101 ILE* 3.0 37.9 - - + +
4052 GLU* 3.7 3.6 - - + +
4062 GLY* 1.3 72.0 - - - +
4082 LEU* 1.3 64.5 + - - +
4092 TYR* 4.5 3.1 - - + +
4432 VAL* 3.3 29.6 - - + -
4442 THR 3.6 2.2 - - - -
4452 PRO* 3.6 28.0 - - + -
4462 ALA* 4.3 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 408 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51 LEU* 2.7 43.0 - - + +
61 LYS 3.5 1.3 - - - -
71 GLY* 3.4 25.8 - - - +
4072 VAL* 1.3 79.3 - - - +
4092 TYR* 1.3 57.8 + - - +
4102 ASN* 5.5 0.5 - - - +
4422 VAL 4.1 0.2 - - - +
4432 VAL* 3.5 2.1 - - - -
4442 THR* 2.8 49.4 + - - +
4452 PRO 5.0 0.2 - - - -
4462 ALA* 5.4 4.3 - - + -
4492 SER* 3.5 34.8 - - - +
4532 ARG* 5.4 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 409 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51 LEU* 2.5 27.3 - - - +
61 LYS* 2.7 32.4 + - + +
81 VAL* 4.5 8.1 - - + -
101 ILE* 5.9 0.2 - - + -
371 ASP* 4.9 7.4 + - - -
391 ASP* 3.4 19.9 - - + +
451 VAL* 3.0 39.0 - - + -
4072 VAL* 4.2 4.0 - - + +
4082 LEU* 1.3 73.2 - - - +
4102 ASN* 1.3 66.0 + - - +
4112 GLN* 3.5 36.8 - - + +
4342 GLU* 3.7 8.6 + - - -
4392 ARG* 5.5 2.1 - - - +
4412 MET* 3.7 35.5 - - + +
4422 VAL 3.6 5.8 - - - -
4432 VAL* 3.2 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 410 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11 MET 4.1 2.4 + - - -
21 VAL* 4.4 2.1 - - - -
41 VAL 2.9 17.8 - - - +
51 LEU* 4.2 4.3 - - + +
4082 LEU 5.5 0.4 - - - +
4092 TYR* 1.3 73.6 - - - +
4112 GLN* 1.3 62.1 + - - +
4132 LEU* 3.8 22.9 - - - +
4222 LEU* 4.0 17.4 - - - +
4262 ARG* 6.0 0.6 - - - +
4412 MET* 3.4 24.9 - - - +
4422 VAL* 3.0 30.7 + - + +
4522 LYS* 5.7 1.4 - - - +
4562 LYS* 2.5 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 411 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41 VAL* 2.4 56.1 + - + +
61 LYS* 4.1 15.2 + - - +
361 GLN* 5.6 6.3 - - - +
4092 TYR* 3.5 44.4 - - + +
4102 ASN* 1.3 78.2 - - - +
4122 PHE* 1.3 84.2 + - + +
4132 LEU* 3.2 11.0 - - - +
4402 LEU 4.1 4.5 - - - -
4412 MET* 3.9 19.1 - - + -
----------------------------------------------------------
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