Contacts of the helix formed by residues 94 - 106 (chain A) in PDB entry 1MF8
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 GLN 94 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 3.2 11.4 + - - +
92A HIS* 3.1 15.2 - - - +
93A GLY* 1.3 69.6 - - - +
95A PHE* 1.3 64.2 + - - +
96A PHE 3.2 3.1 - - - -
97A ASP* 2.9 33.0 + - + +
98A LEU* 3.2 10.0 + - - +
123A GLY* 4.4 7.9 + - - -
125A PHE* 4.8 4.3 - - - -
129A CYS* 4.2 3.3 - - - -
308A ALA* 3.2 24.6 - - - +
309A PRO* 3.3 36.5 + - - +
310A ASN 4.5 1.7 + - - -
311A TYR* 3.5 24.3 - - - -
312A LEU 4.3 2.6 + - - -
339A HIS* 6.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS 4.6 1.1 - - - -
50A LEU* 3.6 38.8 - - + -
51A MET* 3.9 12.3 - - + -
93A GLY 2.7 9.1 + - - -
94A GLN* 1.3 69.9 - - - +
96A PHE* 1.3 78.9 + + + +
98A LEU* 3.0 20.8 + - + +
99A MET* 3.1 50.3 + - + +
125A PHE* 3.4 24.8 - - + +
128A GLU* 3.3 35.0 - - + -
129A CYS* 3.4 19.5 - - - -
132A TYR* 4.1 11.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU 4.4 3.1 - - - -
51A MET* 3.6 53.2 - - + -
53A GLU* 4.9 3.6 - - + -
94A GLN 3.2 1.0 + - - -
95A PHE* 1.3 90.3 - + + +
97A ASP* 1.3 61.2 + - - +
98A LEU 3.3 2.0 - - - -
99A MET* 4.0 11.0 - - + +
100A LYS* 4.1 8.0 + - - +
125A PHE* 4.0 20.9 - + - -
337A SER* 3.5 19.1 + - - -
338A PRO 3.4 27.8 - - - +
339A HIS* 3.9 15.7 - - + +
340A PRO* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 5.5 1.1 - - - +
94A GLN* 2.9 33.6 + - + +
96A PHE* 1.3 79.9 - - - +
98A LEU* 1.3 59.9 + - - +
99A MET 3.5 0.2 - - - -
100A LYS* 3.9 3.8 - - - +
101A LEU* 3.3 7.1 + - - +
307A SER 5.0 3.7 - - - +
309A PRO* 2.8 40.5 - - + +
334A PHE* 3.2 26.6 - - - -
335A ASN 4.1 0.2 - - - +
336A CYS* 3.3 3.5 - - - +
337A SER* 3.2 34.2 + - - +
339A HIS* 4.8 10.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 3.3 38.1 - - + -
94A GLN 3.2 8.9 + - - +
95A PHE* 3.1 12.1 - - + +
97A ASP* 1.3 77.3 - - - +
99A MET* 1.3 76.5 + - + +
100A LYS 3.0 2.0 - - - -
101A LEU* 3.0 17.9 + - + +
102A PHE* 3.1 39.9 + - + -
115A PHE* 4.1 17.9 - - + -
129A CYS* 4.2 26.2 - - + -
132A TYR* 4.4 3.8 - - + -
133A LEU* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 3.4 47.5 + - - +
51A MET* 4.0 17.7 - - + -
95A PHE* 3.1 43.9 + - + +
96A PHE* 4.2 11.2 - - + +
97A ASP 3.5 0.2 - - - -
98A LEU* 1.3 87.6 - - + +
100A LYS* 1.3 57.7 + - - +
102A PHE* 3.7 10.0 + - + +
103A GLU* 3.5 15.9 + - - +
132A TYR* 3.4 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE 4.1 3.0 + - - +
97A ASP 3.9 8.6 + - - +
98A LEU 3.0 0.8 - - - -
99A MET* 1.3 77.4 - - - +
101A LEU* 1.3 65.3 + - - +
102A PHE 2.9 1.8 - - - -
103A GLU* 2.8 44.6 + - - +
104A VAL* 3.0 30.4 + - + +
334A PHE* 3.7 24.9 - - + -
335A ASN 4.8 4.0 - - - +
337A SER* 3.9 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A CYS* 4.1 22.4 - - + -
91A ILE* 3.7 18.4 - - + -
97A ASP 3.3 13.9 + - - +
98A LEU* 3.0 10.2 + - + +
100A LYS* 1.3 78.6 - - - +
102A PHE* 1.3 76.4 + - + +
104A VAL* 3.7 3.6 - - - +
105A GLY* 2.7 30.1 + - - -
113A TYR* 4.3 5.8 - - + -
115A PHE* 4.6 4.3 - - + -
307A SER* 3.5 34.1 - - - +
321A VAL* 3.5 16.9 - - + +
334A PHE* 3.7 16.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 5.8 4.5 - - + +
98A LEU* 3.1 43.6 + - + +
99A MET* 3.8 9.9 - - + +
100A LYS 2.9 0.8 - - - -
101A LEU* 1.3 78.1 - - + +
103A GLU* 1.3 62.1 + - - +
104A VAL 3.1 1.3 - - - -
106A GLY* 3.1 25.9 + - - +
107A SER* 4.1 2.1 + - - -
108A PRO* 4.6 16.2 - - + -
113A TYR* 3.7 29.4 - + - -
115A PHE* 3.7 22.0 - + - -
132A TYR* 3.8 28.9 - + - -
133A LEU* 3.8 22.9 - - + -
136A LEU* 4.1 13.9 - - + -
144A LEU* 5.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A MET 3.5 9.4 + - - +
100A LYS* 2.8 41.8 + - + +
102A PHE* 1.3 79.8 - - - +
104A VAL* 1.3 60.6 + - + +
106A GLY* 4.2 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 3.0 34.1 + - + +
101A LEU* 3.7 5.8 - - - +
103A GLU* 1.3 79.9 - - - +
105A GLY* 1.3 53.2 + - - +
106A GLY* 3.2 5.1 + - - -
321A VAL* 4.5 5.4 - - + -
323A LYS* 2.6 29.3 + - - -
332A ARG* 3.5 58.0 + - + +
333A GLN 5.1 0.7 - - - +
334A PHE* 4.1 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 3.6 24.8 + - - -
101A LEU 2.7 17.2 + - - -
104A VAL* 1.3 73.9 - - - +
106A GLY* 1.3 56.2 + - - +
111A THR* 3.7 10.2 - - - +
113A TYR* 3.0 21.5 + - - -
321A VAL* 4.7 3.6 - - - +
323A LYS* 3.6 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE 3.1 16.2 + - - +
103A GLU 4.2 4.0 - - - -
104A VAL 3.2 5.0 + - - +
105A GLY* 1.3 78.2 - - - +
107A SER* 1.3 68.7 + - - +
108A PRO* 3.2 2.3 - - - +
111A THR* 3.7 5.6 - - - -
113A TYR* 2.6 24.4 + - - -
----------------------------------------------------------
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