Contacts of the helix formed by residues 98 - 109 (chain M) in PDB entry 2W4G
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 HIS 98 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M PHE* 4.4 1.8 - + - -
78M PHE* 3.1 41.7 - + + +
79M SER* 2.8 36.0 + - - -
80M MET* 4.8 0.9 - - - -
96M HIS* 3.3 27.8 + + + -
97M LEU* 1.3 77.4 - - - +
99M GLU* 1.3 67.4 + - - +
100M PRO* 3.2 12.1 - - + -
101M ALA* 3.2 26.2 + - + +
102M VAL* 3.5 20.1 - - - +
701M LEU* 5.2 1.7 - - - +
704M ILE* 4.8 5.2 - - - +
708M ARG* 4.3 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M PHE* 3.9 20.8 - - + -
78M PHE* 5.6 3.4 - - + -
98M HIS* 1.3 74.7 - - - +
100M PRO* 1.3 72.3 - - + +
102M VAL* 3.2 13.8 + - - +
103M LEU* 3.3 12.2 + - - +
692M LEU* 4.2 10.6 - - + +
695M LEU* 5.4 0.3 - - - +
696M ARG* 2.3 43.7 + - - -
701M LEU* 3.6 28.4 - - + +
705M ARG* 4.2 19.2 + - - -
708M ARG* 5.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 100 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M PHE* 3.7 27.8 - - + -
47M PHE* 3.6 45.5 - - + -
78M PHE* 3.8 20.0 - - + -
98M HIS* 3.2 12.3 - - + -
99M GLU* 1.3 94.1 - - + +
101M ALA* 1.3 65.0 + - - +
102M VAL 2.9 0.7 + - - -
103M LEU* 3.0 5.7 + - + +
104M TYR* 2.8 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M PHE* 3.9 15.4 - - + -
81M ASN* 3.5 10.3 - - - +
94M MET* 3.0 35.5 - - + +
96M HIS 3.6 4.3 - - - +
98M HIS* 3.2 28.5 + - + +
99M GLU 3.4 0.6 - - - -
100M PRO* 1.3 79.5 - - - +
102M VAL* 1.3 58.1 + - - +
104M TYR* 4.0 1.0 - - - +
105M ASN* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91M MET* 3.9 32.1 - - + +
94M MET* 4.8 5.4 - - + -
96M HIS 5.7 0.2 - - - +
97M LEU* 5.7 2.7 - - + -
98M HIS 3.5 17.7 + - - +
99M GLU 3.2 8.2 + - - +
100M PRO 2.9 1.2 - - - -
101M ALA* 1.3 78.0 - - - +
103M LEU* 1.3 70.4 + - - +
105M ASN 3.4 0.3 + - - -
106M LEU* 3.3 24.4 + - + +
119M SER* 5.4 0.7 - - - +
695M LEU* 3.8 22.2 - - + -
700M VAL* 4.6 8.1 - - + -
701M LEU* 4.4 11.9 - - + -
704M ILE* 4.3 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M SER* 5.0 0.4 - - - -
47M PHE* 4.8 7.4 - - + -
99M GLU 3.3 8.8 + - - +
100M PRO* 3.0 8.9 + - + +
102M VAL* 1.3 84.7 - - - +
104M TYR* 1.3 78.3 + - + +
106M LEU* 3.1 3.1 + - - +
107M LYS* 3.0 21.1 + - + +
686M MET* 3.5 24.2 - - + -
688M HIS* 4.0 32.3 - - + +
691M VAL* 4.5 15.9 - - + -
692M LEU* 3.6 39.0 - - + -
695M LEU* 4.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M PHE* 3.5 35.9 - + + -
47M PHE* 2.5 39.1 + - + -
48M VAL* 3.1 19.9 - - - +
49M LYS* 4.3 22.4 - - + -
100M PRO* 2.8 23.8 + - + +
101M ALA 4.3 1.6 - - - +
103M LEU* 1.3 86.8 - - + +
105M ASN* 1.3 55.1 + - - +
107M LYS* 3.7 26.2 + - + +
108M GLU* 3.0 43.4 + - + +
688M HIS* 3.6 18.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M TYR 4.5 2.6 - - - +
86M ASP 2.9 28.4 - - - +
87M LYS* 4.3 0.9 - - - -
88M ILE* 3.1 39.4 + - - +
91M MET* 3.4 28.4 - - + +
94M MET* 4.8 7.9 - - + +
101M ALA 3.1 18.9 + - - +
102M VAL 3.4 0.2 + - - -
103M LEU 3.2 0.4 + - - -
104M TYR* 1.3 72.8 - - - +
106M LEU* 1.3 67.4 + - - +
108M GLU* 3.5 3.1 + - - +
109M ARG* 2.9 37.8 + - - +
117M THR* 4.0 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91M MET* 3.1 33.2 - - + -
102M VAL* 3.3 23.9 + - + +
103M LEU* 3.1 7.8 + - - +
105M ASN* 1.3 82.8 - - - +
107M LYS* 1.3 65.2 + - - +
109M ARG* 3.0 14.0 + - - +
110M TYR* 3.2 14.0 + - - +
114M MET 5.0 1.0 - - - +
117M THR* 3.4 26.8 - - + +
124M VAL* 4.4 17.7 - - + -
126M VAL* 5.1 9.7 - - + +
675M ILE* 5.4 1.3 - - + -
686M MET* 4.1 9.6 - - + -
691M VAL* 4.6 9.0 - - + -
695M LEU* 4.4 23.1 - - + -
700M VAL* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M GLU* 5.7 1.0 + - - -
103M LEU* 3.0 9.8 + - + +
104M TYR* 3.7 25.5 + - + +
106M LEU* 1.3 80.2 - - - +
108M GLU* 1.3 66.4 + - + +
110M TYR* 3.2 5.5 + - + +
111M ALA* 3.1 23.7 + - + +
686M MET* 3.0 43.6 + - + +
688M HIS* 2.9 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M LYS* 3.3 31.0 + - - -
86M ASP* 3.7 30.0 - - - +
87M LYS* 4.2 20.7 - - + -
104M TYR* 3.0 31.5 + - + +
105M ASN* 3.5 3.3 + - - +
106M LEU 3.3 0.4 - - - -
107M LYS* 1.3 81.5 - - + +
109M ARG* 1.3 57.0 + - - +
110M TYR 3.0 4.2 + - - -
111M ALA* 3.4 14.5 + - + +
112M ALA* 3.5 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M LEU 4.2 7.9 + - - -
18M ARG* 6.0 0.8 - - - +
87M LYS* 2.9 45.0 + - + +
88M ILE 3.9 4.0 + - - -
89M GLU* 3.7 20.0 + - - +
105M ASN* 2.9 32.7 + - - +
106M LEU 3.0 5.7 + - - +
108M GLU* 1.3 74.4 - - - +
110M TYR* 1.3 51.0 + - - +
112M ALA* 3.9 4.7 - - - -
114M MET* 2.4 82.4 + - + +
116M TYR 2.8 30.1 + - - -
117M THR* 3.4 30.8 - - + +
153M PRO* 4.2 2.8 - - - +
----------------------------------------------------------
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