Contacts of the strand formed by residues 91 - 100 (chain C) in PDB entry 4X7C
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 ALA 91 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 4.0 9.2 - - + -
39C GLN 3.3 26.9 - - - +
40C ALA* 3.7 6.3 - - + +
41C PRO* 5.2 2.5 - - - -
89C ASP 3.2 3.7 + - - +
90C THR* 1.3 77.6 - - - +
92C VAL* 1.3 64.5 + - - +
93C TYR* 3.6 14.9 - - + -
115C GLN* 3.3 9.8 + - - +
116C VAL* 2.7 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 3.1 4.7 - - - +
39C GLN 2.9 35.7 + - - +
91C ALA* 1.3 73.9 - - - +
93C TYR* 1.3 62.5 + - - +
94C TYR* 3.4 42.0 - - + +
112C ARG 4.7 0.9 - - - +
113C GLY* 4.1 3.4 - - - -
114C THR 3.6 20.9 - - - +
115C GLN* 3.6 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLU* 3.6 4.0 - - - +
20C LEU* 4.0 28.7 - - + -
36C TRP* 4.6 7.1 - - + -
37C TYR 3.4 4.9 - - - +
38C ARG* 2.8 43.1 + - + -
48C VAL* 4.0 15.3 - - + -
67C PHE* 4.4 7.5 - + - -
80C LEU* 4.8 4.5 - - + -
82C MET* 3.9 18.4 - - - -
89C ASP* 2.7 34.9 + - - +
91C ALA* 3.6 16.2 - - + -
92C VAL* 1.3 76.4 - - - +
94C TYR* 1.3 61.3 + - - +
113C GLY* 3.2 1.4 - - - -
114C THR* 2.9 38.6 + - - +
116C VAL* 3.7 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLU* 3.5 2.9 - - - -
36C TRP* 3.3 5.4 - - - -
37C TYR* 2.7 47.1 + - + +
39C GLN* 4.3 17.0 + - + +
45C ARG* 3.7 35.8 + - - -
92C VAL* 3.4 39.2 - - + +
93C TYR* 1.3 72.8 - - - +
95C CYS* 1.3 66.8 + - - +
96C LYS* 3.8 2.5 + - + +
110C ARG* 5.7 3.6 - - + -
111C GLY 3.7 11.7 - - - +
112C ARG 3.4 26.7 - - - -
113C GLY* 3.7 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 4.2 6.3 - - + -
6C GLU* 2.7 22.8 + - + +
22C CYS* 2.0 54.7 - - + -
34C MET* 4.1 10.3 - - - -
35C GLY 3.3 11.0 - - - -
36C TRP* 3.7 13.1 - - + -
78C VAL* 4.8 2.7 - - - -
94C TYR* 1.3 75.3 - - - +
96C LYS* 1.3 63.0 + - - +
110C ARG* 3.4 5.5 - - - +
111C GLY 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A PHE* 3.8 18.4 - - + +
4C LEU* 4.3 1.8 - - - -
34C MET* 3.2 4.7 - - - +
35C GLY 2.8 37.2 + - - +
37C TYR* 3.4 48.6 + - + -
94C TYR* 4.7 1.1 - - + +
95C CYS* 1.3 78.2 - - - +
97C ARG* 1.3 64.6 + - - +
98C GLU* 3.1 35.0 + - - -
108C GLY* 6.1 0.2 - - - -
109C SER 3.5 10.1 - - - +
110C ARG* 4.4 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C VAL* 4.4 4.3 - - - -
4C LEU* 4.0 9.6 - - + +
24C ALA* 3.5 25.2 - - - +
28C ILE* 3.7 15.1 - - - +
29C PHE 3.3 15.0 + - - -
32C TYR* 3.4 20.9 - - - +
33C ALA 3.3 4.9 - - - +
34C MET* 3.4 40.0 - - + -
76C ASN* 3.3 28.0 + - - +
96C LYS* 1.3 77.2 - - - +
98C GLU* 1.3 69.9 + - - +
99C ASP* 2.9 38.4 + - - +
107C SER 3.8 0.3 - - - +
108C GLY* 3.3 4.2 - - - -
109C SER* 2.8 48.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ASN* 2.9 23.1 + - - -
524A PHE* 3.4 26.4 - - + -
32C TYR* 3.1 8.3 - - - +
33C ALA 2.8 33.4 + - - -
96C LYS* 3.1 25.6 + - - -
97C ARG* 1.3 73.0 - - - +
99C ASP* 1.3 62.4 + - - +
100C TYR* 3.3 26.6 - - + +
106C PRO* 3.6 11.6 - - - +
107C SER 3.5 1.6 - - - -
108C GLY* 3.6 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C VAL* 3.8 16.8 - - + +
27C SER 4.9 1.3 - - - +
28C ILE* 3.5 5.7 - - - -
29C PHE* 2.8 45.3 + - + +
31C ILE 4.0 1.3 - - - -
32C TYR* 4.0 0.7 - - - +
97C ARG* 2.9 44.8 + - - +
98C GLU* 1.3 73.6 - - - +
100C TYR* 1.3 61.6 + - - +
101C SER 4.4 0.2 + - - -
105C PRO 4.7 0.7 - - - +
106C PRO* 3.6 3.5 - - - +
107C SER* 2.8 46.0 + - - +
109C SER* 4.7 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A SER* 3.6 16.7 + - - -
520A TRP 3.2 22.7 - - - +
521A VAL* 3.5 17.3 - - + -
522A ASN* 2.5 31.0 + - - -
524A PHE* 3.5 3.8 - - - +
525A TYR* 3.5 30.2 + + + -
29C PHE* 3.4 21.7 - - - +
31C ILE* 2.9 18.9 + - + +
32C TYR* 3.5 23.6 - - - -
33C ALA* 3.6 21.8 - - + +
98C GLU* 3.3 19.1 - - + +
99C ASP* 1.3 75.7 - - - +
101C SER* 1.3 62.3 + - - +
106C PRO* 3.7 23.3 - - + -
----------------------------------------------------------
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