Contacts of the strand formed by residues 103 - 107 (chain Y) 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 THR 103 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Y LEU* 3.8 19.3 - - + +
10Y CYS* 4.9 4.0 - - + -
90Y PHE* 4.4 18.2 - - + -
101Y HIS 3.4 9.4 + - - -
102Y PRO* 1.3 74.1 + - - +
104Y LEU* 1.4 59.9 + - - +
105Y LEU* 3.7 29.2 + - + +
123Y MET* 4.6 7.2 - - - -
129Y VAL* 3.4 18.9 - - - +
131Y ALA 2.9 11.6 + - - -
132Y MET* 3.2 28.7 - - - +
133Y TYR 3.3 1.9 + - - -
356Y TRP* 3.8 3.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Y LEU 2.9 15.9 + - - +
9Y VAL* 3.3 22.2 - - + -
10Y CYS* 2.9 25.8 + - - +
103Y THR* 1.4 70.1 - - - +
105Y LEU* 1.3 79.3 + - - +
106Y THR* 4.1 9.4 - - + -
133Y TYR* 3.5 31.9 - - + +
135Y ALA* 4.2 7.9 - - + -
140Y LEU* 4.4 0.2 - - + -
343Y GLY* 4.3 11.0 - - - +
346Y LEU* 4.2 16.6 - - + -
347Y ALA* 4.2 14.1 - - + -
352Y PHE* 4.1 11.9 - - + -
356Y TRP* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Y CYS* 3.5 34.3 - - + +
12Y ASN* 4.3 7.9 - - - +
86Y TRP* 4.4 9.0 - - + +
90Y PHE* 6.1 0.7 - - + -
103Y THR* 3.9 19.5 - - + +
104Y LEU* 1.3 80.8 - - - +
106Y THR* 1.3 64.9 + - - +
119Y MET* 3.7 28.5 - - + -
123Y MET* 3.7 35.2 - - + -
132Y MET* 3.7 13.9 - - + -
133Y TYR 2.8 10.0 + - - +
134Y VAL* 3.4 3.7 - - + -
135Y ALA 2.9 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 106 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Y VAL* 5.4 2.2 - - + -
10Y CYS 3.4 10.0 + - - +
11Y ASP* 2.9 30.4 + - + +
12Y ASN* 3.7 19.2 + - - +
104Y LEU* 4.1 5.8 - - + -
105Y LEU* 1.3 80.3 - - - +
107Y GLU* 1.3 60.5 + - - +
119Y MET* 4.1 7.8 - - - +
134Y VAL* 4.4 3.1 - - - -
135Y ALA 3.3 6.5 - - - -
137Y GLN* 3.8 16.3 + - - +
140Y LEU* 3.4 32.5 - - + -
339Y VAL* 4.2 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74Y GLY 5.8 0.2 - - - -
106Y THR* 1.3 75.4 - - - +
108Y ALA* 1.3 66.6 + - - +
109Y PRO 5.3 0.7 - - - +
111Y ASN* 2.9 43.3 + - - +
116Y ARG* 3.1 51.5 + - - +
119Y MET* 5.0 3.8 - - - -
134Y VAL* 3.6 13.6 - - + +
135Y ALA 3.0 11.8 + - - +
136Y ILE* 3.7 14.3 - - + +
137Y GLN* 3.0 37.0 + - - +
----------------------------------------------------------
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