Contacts of the helix formed by residues 86 - 96 (chain Y) in PDB entry 6CP3
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 86 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71Y ILE* 4.8 5.5 - - + +
75Y VAL* 3.9 27.6 - - + -
80Y ASN* 6.2 0.2 - - - -
81Y LEU* 3.5 31.2 + - + +
83Y GLY* 3.0 26.9 - - - +
85Y VAL* 1.3 81.3 - - - +
87Y ASN* 1.3 63.1 + - + +
89Y LEU* 4.0 15.9 + - - +
90Y LYS* 4.0 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ARG 3.7 14.1 + - - +
18C ILE* 3.7 22.8 + - - +
19C LYS 4.5 1.2 + - - -
20C GLY* 3.9 19.2 - - - -
83Y GLY 3.9 10.8 - - - +
84Y TYR* 3.2 8.9 + - + +
86Y VAL* 1.3 82.3 - - + +
88Y LEU* 1.3 64.5 + - - +
89Y LEU 3.2 0.4 - - - -
90Y LYS* 3.2 20.7 + - - +
91Y VAL* 3.5 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 6.5 0.4 - - + -
18C ILE* 3.8 30.9 - - + +
19Y TYR* 5.0 15.3 - - + +
23Y LEU* 4.6 23.3 - - + -
84Y TYR 3.0 15.7 + - - +
85Y VAL* 4.4 8.5 - - - +
86Y VAL 3.5 0.2 - - - -
87Y ASN* 1.3 76.1 - - - +
89Y LEU* 1.3 70.6 + - + +
91Y VAL* 3.2 16.3 + - + -
92Y LEU* 3.0 40.6 + - + -
101Y PHE* 6.0 5.8 - - + -
104Y ILE* 5.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Y VAL* 5.3 6.1 - - + -
71Y ILE* 3.5 40.4 - - + +
74Y ILE* 4.7 19.5 - - + -
75Y VAL* 5.2 3.8 - - + -
85Y VAL 3.8 17.1 + - - +
86Y VAL* 4.0 12.0 + - - +
87Y ASN 3.2 0.4 - - - -
88Y LEU* 1.3 83.5 - - + +
90Y LYS* 1.3 51.6 + - - +
92Y LEU* 3.1 6.8 + - + +
93Y SER* 2.6 38.2 + - - -
98Y LEU* 3.7 20.1 - - + +
101Y PHE* 4.2 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Y ASN* 5.2 8.1 - - - +
71Y ILE* 4.8 6.4 - - + +
86Y VAL 4.0 5.4 + - - +
87Y ASN* 3.2 16.0 + - - +
88Y LEU 3.2 0.2 - - - -
89Y LEU* 1.3 78.0 - - - +
91Y VAL* 1.3 56.8 + - + +
93Y SER* 2.7 25.7 + - - +
94Y GLU* 2.8 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 4.7 9.9 - - + -
17C ARG* 3.8 49.4 - - + +
18C ILE* 5.3 1.3 - - + +
19Y TYR* 4.4 4.3 - - + +
87Y ASN* 3.5 10.2 + - - +
88Y LEU* 3.2 22.0 + - + +
90Y LYS* 1.3 77.9 - - + +
92Y LEU* 1.3 63.3 + - + +
94Y GLU* 3.2 9.6 + - - +
95Y ASN* 2.6 50.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y TYR* 2.3 52.7 - - + -
88Y LEU* 3.0 29.9 + - + +
89Y LEU* 3.5 11.4 - - + +
91Y VAL* 1.3 78.3 - - + +
93Y SER* 1.3 57.1 + - - +
95Y ASN* 4.1 2.0 - - - +
96Y ASN* 2.6 30.7 + - - -
97Y ARG* 2.8 66.3 + - + +
98Y LEU* 3.6 14.7 + - + +
101Y PHE* 6.0 4.5 - - + -
104Y ILE* 5.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Y SER 5.2 0.7 - - - +
64Y LEU* 3.8 13.8 - - - +
67Y ARG* 4.3 25.0 - - - +
68Y ASN* 4.3 18.2 - - - +
71Y ILE* 4.1 19.3 - - - -
89Y LEU 2.6 20.3 + - - -
90Y LYS* 2.7 17.7 + - - -
92Y LEU* 1.3 72.9 - - - +
94Y GLU* 1.3 62.9 + - - +
96Y ASN* 3.4 12.8 + - - +
98Y LEU* 4.8 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ARG* 2.8 41.1 + - - +
56D GLU* 5.3 4.5 - - - +
64Y LEU* 3.7 22.0 - - + +
90Y LYS 2.8 11.9 + - - +
91Y VAL* 3.5 5.7 - - - +
93Y SER* 1.3 82.5 + - - +
95Y ASN* 1.3 87.0 + - - +
96Y ASN* 3.5 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLN* 4.6 14.6 + - - +
8C THR* 4.9 6.2 + - - +
9C GLU* 4.3 17.0 + - - +
14C LEU* 4.6 3.5 - - - +
17C ARG* 3.5 18.7 + - - +
56D GLU* 5.0 1.0 - - - +
19Y TYR* 2.7 29.2 + - + +
91Y VAL* 2.6 23.7 + - - +
92Y LEU* 3.3 5.4 + - - +
94Y GLU* 1.3 93.4 + - - +
96Y ASN* 1.3 62.6 - - - +
97Y ARG* 2.9 13.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 96 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLU* 3.4 33.0 + - - +
59Y ASN 5.2 1.4 - - - +
60Y PRO* 4.1 34.9 + - - +
63Y SER 4.5 12.9 - - - +
67Y ARG* 5.4 4.2 - - - +
92Y LEU 2.6 14.9 + - - -
93Y SER* 3.4 9.2 + - - +
94Y GLU 3.2 4.3 - - - +
95Y ASN* 1.3 74.0 - - - +
97Y ARG* 1.3 54.5 + - - +
98Y LEU* 3.1 13.5 + - - +
99Y GLY 4.6 2.1 + - - -
----------------------------------------------------------
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