Contacts of the helix formed by residues 87 - 101 (chain M) in PDB entry 6FF7
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 VAL 87 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M ARG 4.8 1.1 - - - -
86M CYS* 1.3 81.5 - - - +
88M THR* 1.3 70.1 + - - +
89M ASP 3.6 1.1 - - - -
90M PRO* 3.9 7.7 - - - +
91M ALA* 3.7 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M CYS* 4.7 1.2 - - - +
87M VAL* 1.3 78.0 - - - +
89M ASP* 1.3 56.5 + - - +
91M ALA* 2.8 31.3 + - - +
92M TYR* 2.9 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M ARG 5.8 2.2 - - - +
86M CYS* 5.5 6.1 - - + +
87M VAL 3.6 1.4 - - - +
88M THR* 1.3 77.4 - - - +
90M PRO* 1.3 57.3 - - - +
92M TYR* 3.3 6.6 + - - +
93M GLU* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 90 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M ARG* 5.1 12.4 - - + +
82M VAL* 3.8 39.9 - - + +
83M LYS* 5.0 2.2 - - - +
85M ARG 4.8 5.6 - - - +
87M VAL 3.9 7.4 - - - +
88M THR 3.1 0.8 - - - -
89M ASP* 1.3 77.3 - - - +
91M ALA* 1.3 57.6 + - - +
93M GLU* 3.8 4.7 - - + +
94M ASP* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M ARG* 6.3 0.4 - - - -
87M VAL 3.7 9.7 + - - +
88M THR* 2.8 15.7 + - - +
90M PRO* 1.3 76.0 - - - +
92M TYR* 1.3 55.9 + - - +
94M ASP* 4.3 3.3 - - - +
95M VAL* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 92 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88M THR* 2.9 17.2 + - - +
89M ASP* 3.9 8.1 - - - +
91M ALA* 1.3 75.0 - - - +
93M GLU* 1.3 61.3 + - - +
95M VAL* 4.6 2.9 - - - -
96M ASN* 2.8 32.7 + - - +
945U GLU* 4.6 5.6 - - - +
946U GLU* 3.7 3.4 - - - +
949U SER* 3.2 34.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M PRO* 5.8 6.7 - - + -
53M LEU* 5.5 11.7 - - + -
89M ASP 2.9 16.8 + - - +
90M PRO* 3.3 6.0 + - + +
92M TYR* 1.3 75.6 - - - +
94M ASP* 1.3 60.4 + - - +
96M ASN* 3.8 3.3 - - - +
97M ASN* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 94 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75M LEU* 4.1 32.8 - - + +
78M ARG* 6.5 0.2 - - + -
79M ARG* 4.3 11.0 - - + -
90M PRO 2.9 17.7 + - - +
91M ALA* 4.3 2.9 - - - +
93M GLU* 1.3 74.4 - - - +
95M VAL* 1.3 61.4 + - - +
97M ASN* 3.8 4.1 - - - +
98M CYS* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91M ALA 2.9 21.2 + - - +
92M TYR* 4.4 2.9 - - - +
94M ASP* 1.3 77.3 - - - +
96M ASN* 1.3 59.0 + - - +
98M CYS* 4.0 4.2 - - - +
99M HIS 2.9 23.4 + - - -
116M TYR* 5.4 11.7 - - + -
942U SER* 3.2 16.4 - - - +
945U GLU* 5.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 96 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M TYR 2.8 17.0 + - - +
93M GLU* 4.0 4.0 - - - +
95M VAL* 1.3 78.1 - - - +
97M ASN* 1.3 56.6 + - - +
99M HIS* 3.9 0.5 - - - +
100M GLU* 2.9 31.9 + - - +
942U SER 3.5 8.2 + - - +
943U ARG* 4.7 0.3 - - - -
946U GLU* 1.8 48.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 97 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M LEU* 6.5 0.9 - - + -
57M TYR* 6.1 9.6 - - + +
71M TRP* 6.0 1.1 - - + +
75M LEU* 5.5 7.0 - - + -
93M GLU 2.9 19.4 + - - +
94M ASP* 3.9 5.4 - - - +
96M ASN* 1.3 75.9 - - - +
98M CYS* 1.3 61.9 + - - +
100M GLU* 3.8 3.9 - - - +
101M ARG* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 98 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72M TYR* 5.9 7.0 - - + +
75M LEU* 5.6 6.6 - - + +
94M ASP 2.9 18.8 + - - +
95M VAL* 4.0 5.2 - - - +
97M ASN* 1.3 76.7 - - - +
99M HIS* 1.3 62.1 + - - +
101M ARG* 4.0 4.5 - - - +
102M ALA* 3.3 23.2 + - - +
109M MET* 5.5 0.7 - - - +
112M LEU* 5.0 16.6 - - + -
938U TYR 4.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 99 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M VAL 2.9 6.7 + - - +
98M CYS* 1.3 75.8 - - - +
100M GLU* 1.3 63.2 + - - +
102M ALA 3.5 4.5 + - - -
103M PHE 3.8 1.9 - - - +
938U TYR 2.9 11.1 - - - +
939U GLN* 3.2 27.2 - - - +
942U SER* 1.0 69.9 - - - +
943U ARG 3.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M TYR* 5.7 11.2 - - + +
60M ALA* 6.3 0.4 - - - -
61M LEU* 5.5 11.5 - - + +
96M ASN 2.9 21.2 + - - +
97M ASN* 4.0 4.5 - - - +
99M HIS* 1.3 76.9 - - - +
101M ARG* 1.3 60.9 + - - +
102M ALA 3.4 0.5 + - - -
103M PHE* 3.6 11.0 + - - -
919U LEU* 5.2 4.3 - - - +
939U GLN 4.9 0.2 - - - -
943U ARG* 4.5 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M ALA* 4.8 22.9 - - + +
65M PRO* 4.3 15.6 - - - +
68M TYR* 4.0 32.8 - - + +
71M TRP* 5.1 7.6 - - + -
97M ASN 2.9 18.8 + - - +
98M CYS* 4.0 6.1 - - - +
99M HIS 3.4 0.2 - - - -
100M GLU* 1.3 76.7 - - - +
102M ALA* 1.3 58.2 + - - +
103M PHE* 3.3 1.6 + - - +
----------------------------------------------------------
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