Contacts of the strand formed by residues 94 - 103 (chain C) in PDB entry 6P59
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 LYS 94 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 3.6 12.5 - - - +
91C GLU* 3.2 57.7 + - + +
92C ALA 3.3 4.1 - - - +
93C GLY* 1.3 82.1 + - - +
95C VAL* 1.3 59.0 + - - +
96C TYR* 4.5 20.0 + - + +
113C TRP* 4.9 24.4 - - + -
114C ILE 3.5 9.2 - - - +
115C ASP* 5.0 8.3 - - - +
116C LEU* 3.3 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PHE* 3.9 20.2 - - + -
48C CYS* 5.3 0.9 - - - -
86C VAL* 4.2 15.0 - - + -
87C ASP 3.6 10.5 - - - +
88C LEU* 3.5 22.9 - - + -
94C LYS* 1.3 75.6 - - - +
96C TYR* 1.3 76.3 + - - +
97C LEU* 4.4 8.6 - - + +
113C TRP* 3.0 4.5 - - - -
114C ILE* 2.9 55.3 + - + +
116C LEU* 3.6 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TYR 3.9 0.6 - - - +
86C VAL* 3.8 2.1 - - - -
87C ASP* 3.0 36.1 + - + +
90C ARG* 3.5 48.2 - - + +
91C GLU* 3.4 29.4 + - + -
94C LYS* 4.5 16.4 + - + +
95C VAL* 1.3 81.6 - - - +
97C LEU* 1.3 64.9 + - - +
111C LYS* 6.4 0.9 - - + -
112C GLY 3.2 15.3 - - - -
113C TRP* 4.2 27.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ILE* 4.2 13.7 - - + -
57C PHE* 3.6 47.8 - - + -
68C PHE* 4.2 11.0 - - + -
85C TYR 3.3 4.5 - - - -
86C VAL* 4.0 27.6 - - + -
95C VAL* 4.4 9.0 - - + +
96C TYR* 1.3 83.3 - - - +
98C LYS* 1.3 61.2 - - - +
110C TRP* 3.7 27.8 - - + -
111C LYS* 3.3 8.5 - - - +
112C GLY 2.6 32.9 + - - +
114C ILE* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PHE* 3.6 7.0 - - - -
84C GLU* 4.6 14.8 + - + +
85C TYR* 2.8 64.1 + - + +
97C LEU* 1.3 74.9 - - - +
99C ALA* 1.3 64.8 + - - +
100C PRO* 4.5 5.6 - - + -
109C ILE* 4.5 23.6 - - + -
110C TRP 3.3 7.4 - - - +
111C LYS* 5.2 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 4.3 11.2 - - + -
68C PHE* 4.3 4.7 - - + -
98C LYS* 1.3 77.9 - - - +
100C PRO* 1.3 65.9 - - - +
101C MET* 3.7 10.0 + - + +
109C ILE* 3.7 3.1 - - - -
110C TRP* 2.8 46.9 + - + +
8F VAL* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C GLN* 3.9 10.2 + - - -
80C THR* 6.0 0.4 - - - +
85C TYR* 3.0 48.9 - - + +
98C LYS* 4.5 6.7 - - + -
99C ALA* 1.3 83.5 - - - +
101C MET* 1.3 65.2 + - - +
108C VAL 3.6 6.5 - - - +
109C ILE* 3.5 20.9 - - + -
128C ASP* 5.0 2.2 - - - +
131C ARG* 3.6 14.1 + - - +
8F VAL* 4.0 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 5.3 4.3 - - + -
66C LEU* 3.6 36.8 - - + -
79C GLN* 4.1 16.4 - - - +
99C ALA* 3.9 12.3 - - + +
100C PRO* 1.3 76.6 - - - +
102C ILE* 1.3 65.3 + - - +
103C LEU* 4.0 20.6 - - + -
107C CYS* 3.8 1.4 - - - -
108C VAL* 2.9 42.4 + - + +
110C TRP* 4.0 20.0 - - + -
125C LEU* 6.0 0.7 - - + -
131C ARG* 3.3 10.2 + - - +
8F VAL* 4.8 4.7 - - - +
10F PRO* 3.5 29.8 - - + -
104F ASP* 4.4 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ARG* 5.5 1.6 - - + +
79C GLN* 5.5 0.2 + - - -
101C MET* 1.3 75.3 - - - +
103C LEU* 1.3 59.8 + - - +
105C GLY* 3.8 21.1 - - - +
106C VAL 3.5 6.3 - - - +
107C CYS* 4.2 10.3 - - - +
131C ARG* 3.4 42.8 - - - +
135C GLU* 4.3 20.4 - - + +
101F TYR* 3.9 7.6 - - + +
102F PHE* 3.1 24.0 - - + +
103F THR* 3.2 21.5 - - - +
104F ASP* 2.6 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PHE* 3.9 6.6 - - + -
18C PHE* 3.7 41.1 - - + -
21C LEU* 4.0 27.1 - - + -
101C MET* 4.3 13.2 - - + -
102C ILE* 1.3 76.1 - - - +
104C ASN* 1.3 72.8 + - - +
105C GLY 3.2 0.2 - - - -
106C VAL* 2.8 31.4 + - - +
108C VAL* 3.7 24.2 - - + -
125C LEU* 4.4 6.1 - - + -
10F PRO* 3.7 29.2 - - + -
104F ASP* 3.3 4.7 - - + -
----------------------------------------------------------
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