Contacts of the strand formed by residues 297 - 300 (chain 4) in PDB entry 1MVW
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 297 (chain 4).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1514 ILE* 3.4 19.7 + - - +
1534 LEU* 4.5 14.3 - - - +
2784 THR* 3.2 33.9 + - - +
2824 ILE* 4.6 2.1 - - - +
2934 LEU 3.7 3.3 + - - +
2944 TYR* 5.0 2.3 - - - +
2964 ASN* 1.3 70.5 - - - +
2984 VAL* 1.3 62.3 + - - +
2994 MET* 4.8 2.6 - - - -
3134 MET* 4.4 12.5 - - - +
3174 ILE* 3.9 9.5 - - - +
3284 LYS 2.9 15.4 + - - +
3294 ILE* 3.5 25.9 - - + +
3304 ILE 2.7 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 298 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1414 SER* 4.5 9.6 - - - +
1424 LEU* 3.7 33.7 - - + -
1454 SER* 3.5 27.8 - - - +
1474 ARG* 4.3 8.7 - - - -
1514 ILE 2.9 7.3 + - - +
1524 VAL* 3.1 20.3 - - + +
1534 LEU* 2.9 25.3 + - - +
2964 ASN 3.4 2.9 + - - +
2974 ASN* 1.3 75.0 - - - +
2994 MET* 1.3 73.3 - - - +
3004 SER* 5.3 0.2 - - - -
3304 ILE* 3.3 17.9 - - + +
3324 PRO* 5.3 4.0 - - + -
3384 SER* 5.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 299 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1534 LEU* 3.6 35.9 - - + -
2974 ASN* 4.8 6.1 - - - -
2984 VAL* 1.3 78.3 - - - +
3004 SER* 1.3 62.7 + - - +
3044 THR* 3.8 18.2 - - - +
3094 ILE* 4.3 13.9 - - + -
3104 ALA* 4.0 14.8 - - - -
3134 MET* 4.8 11.0 - - - -
3294 ILE* 3.6 31.4 - - + -
3304 ILE 2.8 11.7 + - - +
3314 ALA* 3.4 29.4 - - + -
3324 PRO* 3.9 11.1 - - - +
3354 ARG* 3.8 13.4 - - - +
3384 SER* 4.4 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 300 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1414 SER* 3.0 34.4 + - - -
1524 VAL* 3.6 4.8 - - - +
1534 LEU 3.1 9.0 + - - +
1544 ASP* 3.0 22.6 + - - +
1554 SER 3.1 21.8 + - - -
2984 VAL 4.2 0.2 + - - -
2994 MET* 1.3 78.2 - - - +
3014 GLY* 1.3 59.5 + - - +
3044 THR* 3.3 10.4 - - - +
3354 ARG* 4.0 5.4 - - - -
3384 SER* 3.7 14.6 - - - -
3394 VAL* 5.0 2.0 - - - -
----------------------------------------------------------
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