Contacts of the helix formed by residues 92 - 108 (chain I) in PDB entry 7C97
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 TYR 92 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D TYR* 4.3 3.8 + - - -
81D ARG* 3.1 58.9 + - + +
82D GLY* 5.0 3.4 - - - +
90I PRO* 3.7 3.1 - - + +
91I VAL* 1.3 95.2 - - + +
93I PRO* 1.3 57.3 - - + +
94I VAL* 3.0 9.1 + - + +
95I ALA* 3.0 18.5 + - + +
96I ARG* 2.7 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 93 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLY* 3.6 30.1 - - - +
83D VAL* 4.7 3.6 - - + +
91I VAL 3.4 9.9 - - - +
92I TYR* 1.3 82.3 - - + +
94I VAL* 1.3 60.8 + - + +
96I ARG* 3.9 11.8 - - + +
97I GLY 3.3 9.9 + - - -
78J TYR* 3.3 23.1 - - + -
81J GLU* 3.7 33.9 - - + +
82J ARG* 4.0 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLY* 5.8 2.0 - - - +
91D GLU* 5.1 0.9 - - - +
92I TYR* 3.0 6.0 - - + -
93I PRO* 1.3 80.9 - - + +
95I ALA* 1.3 62.5 + - - +
97I GLY* 3.2 11.8 + - - -
98I GLU* 3.7 22.1 + - - +
66J GLU* 3.7 23.8 - - - +
67J LEU* 3.5 27.7 - - + +
78J TYR* 4.4 1.3 - - - +
82J ARG* 3.8 35.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I PRO* 4.2 17.9 - - + +
92I TYR* 3.0 21.8 + - + +
94I VAL* 1.3 78.6 - - - +
96I ARG* 1.3 59.0 + - - +
97I GLY 3.4 0.2 - - - -
98I GLU* 4.4 12.9 - - - +
99I SER* 3.2 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I GLU* 5.9 0.2 + - - -
81I GLU* 4.3 17.0 + - - -
89I MET* 3.8 28.0 - - + +
90I PRO* 3.0 36.5 + - + +
91I VAL* 4.0 14.5 + - - +
92I TYR 2.7 17.1 + - - +
93I PRO* 4.0 7.8 - - + +
94I VAL 3.2 0.2 - - - -
95I ALA* 1.3 73.6 - - - +
97I GLY* 1.3 66.4 + - - +
99I SER* 3.8 4.7 - - - -
100I ARG* 3.2 57.8 + - - +
81J GLU* 2.3 46.0 + - - +
100J ARG* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I PRO 3.3 10.7 + - - -
94I VAL 3.2 9.0 + - - -
96I ARG* 1.3 77.9 - - - +
98I GLU* 1.3 57.8 + - - +
100I ARG* 2.8 25.5 + - - +
101I LEU* 3.0 9.2 + - - +
67J LEU* 5.6 0.7 - - - -
69J LEU* 4.3 15.3 - - - -
74J ILE* 3.9 8.9 - - - +
78J TYR* 4.9 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I VAL* 3.7 21.3 + - - +
95I ALA* 4.2 11.7 + - - +
97I GLY* 1.3 73.4 - - - +
99I SER* 1.3 55.1 + - - +
101I LEU* 2.5 32.0 + - + +
102I TYR* 2.8 46.2 + - + -
67J LEU* 3.0 36.3 - - + +
68J THR 5.6 1.6 - - - +
69J LEU* 4.5 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 99 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I MET* 2.9 31.4 - - - +
90I PRO* 4.2 6.6 - - - +
95I ALA 3.2 21.9 + - - -
96I ARG* 3.8 4.0 - - - -
97I GLY 3.1 1.2 - - - -
98I GLU* 1.3 77.0 - - - +
100I ARG* 1.3 58.8 + - - +
102I TYR* 4.4 10.2 + - - -
103I MET* 3.3 26.7 + - - +
155I SER* 5.0 2.6 + - - -
157I VAL* 4.5 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I ARG* 6.0 7.6 - - - +
77I GLU* 3.8 21.4 + - - +
89I MET* 5.2 12.4 - - + +
96I ARG* 3.2 52.1 + - - +
97I GLY* 2.8 13.2 + - - +
99I SER* 1.3 76.0 - - - +
101I LEU* 1.3 59.5 + - - +
102I TYR 3.7 0.2 - - - -
103I MET* 4.1 23.6 - - + +
104I HIS* 3.7 11.3 + - - +
73J ARG 5.8 0.7 - - - -
74J ILE* 3.2 32.3 - - + +
77J GLU* 4.0 22.9 + - - +
81J GLU* 5.6 2.0 - - - +
100J ARG* 3.1 30.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I GLY 3.0 5.0 + - - +
98I GLU* 2.5 34.0 + - + +
100I ARG* 1.3 71.0 - - - +
102I TYR* 1.3 66.7 + - + +
103I MET 3.2 1.3 - - - -
104I HIS* 3.2 3.9 + - + +
105I ARG* 2.9 67.5 + - + +
68J THR* 4.7 7.4 - - - +
69J LEU* 4.6 11.7 - - + -
70J TRP* 3.8 39.3 - - + +
74J ILE* 3.3 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 102 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I GLU* 2.8 50.9 + - + +
99I SER* 4.4 5.6 + - - +
101I LEU* 1.3 83.8 - - + +
103I MET* 1.3 62.7 + - - +
105I ARG* 3.0 22.4 + - - +
106I ILE* 3.0 23.5 + - + +
149I PHE* 4.0 32.8 - + + -
150I LEU* 4.1 22.8 - - + +
157I VAL* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 103 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I ARG* 4.7 19.1 - - + -
76I MET* 5.7 2.7 - - + -
89I MET* 4.8 7.4 - - + -
99I SER 3.3 22.4 - - - +
100I ARG* 4.1 23.6 - - + +
101I LEU 3.2 0.8 - - - -
102I TYR* 1.3 74.9 - - - +
104I HIS* 1.3 58.9 + - - +
106I ILE* 3.1 8.5 + - - +
107I GLU* 3.0 37.5 + - - +
156I LEU* 4.3 24.2 - - + -
157I VAL* 4.4 12.1 - - + -
160I TYR* 3.4 43.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 104 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I ARG* 5.0 11.6 + - - -
100I ARG 3.7 3.9 + - - +
101I LEU* 3.2 8.6 + - + +
103I MET* 1.3 80.0 - - - +
105I ARG* 1.3 58.3 + - + +
106I ILE 3.1 2.9 + - - -
107I GLU* 4.1 7.5 - - - +
108I LYS* 3.4 55.3 + - + +
56J ASN* 5.7 1.3 - - - -
70J TRP* 4.4 18.3 - + - -
71J GLU* 3.1 48.0 + - + +
74J ILE* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I LEU* 2.9 43.1 + - + +
102I TYR* 3.0 18.3 + - - +
104I HIS* 1.3 76.9 - - + +
106I ILE* 1.3 60.9 + - + +
108I LYS* 5.3 0.4 - - - -
109I ASP* 3.0 31.8 + - + +
110I TRP* 5.2 2.8 + - - -
55J PRO* 3.2 27.9 - - - +
56J ASN* 5.5 2.9 + - - +
70J TRP* 3.5 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102I TYR* 3.0 22.3 + - + +
103I MET* 3.1 6.0 + - - +
105I ARG* 1.3 82.5 - - + +
107I GLU* 1.3 58.3 + - - +
108I LYS 3.1 4.7 - - - -
109I ASP 3.8 0.4 - - - -
110I TRP* 2.9 46.3 + - + +
111I TYR* 3.0 10.6 + - - +
149I PHE* 5.5 7.4 - - + -
157I VAL* 4.7 8.3 - - + +
160I TYR* 4.2 23.6 - - + +
161I LEU* 3.6 30.1 - - + -
164I LEU* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I TYR* 4.6 7.8 + - - -
71I GLU* 5.4 2.9 - - - +
72I SER* 4.9 3.4 + - - -
73I ARG* 4.4 24.3 + - - +
103I MET* 3.0 20.5 + - - +
104I HIS* 4.7 6.6 - - - +
106I ILE* 1.3 74.3 - - - +
108I LYS* 1.3 69.8 + - + +
111I TYR* 3.4 44.7 - - + +
112I THR* 5.0 2.1 - - - +
160I TYR* 2.5 46.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 108 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I HIS* 3.4 45.2 + - + +
105I ARG* 5.0 0.7 - - - -
106I ILE 3.1 0.4 - - - -
107I GLU* 1.3 87.7 - - + +
109I ASP* 1.3 59.1 + - - +
111I TYR 5.0 0.4 - - - -
112I THR* 4.3 21.0 + - + +
----------------------------------------------------------
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