Contacts of the helix formed by residues 115 - 133 (chain Z) 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 ASN 115 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077 GLU* 5.9 0.4 - - - -
112Z GLN 4.8 1.7 - - - +
114Z GLN* 1.3 81.5 + - + +
116Z VAL* 1.3 70.1 + - - +
117Z ALA 3.6 1.3 - - - -
118Z GLU* 3.8 22.7 - - + +
119Z THR* 3.3 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147 LYS* 2.8 20.3 + - + +
177 SER* 5.4 13.7 - - - +
7U PRO* 4.6 19.5 - - + +
112Z GLN 3.3 26.5 - - - +
113Z LEU* 3.7 29.1 + - + +
114Z GLN 3.4 3.6 - - - -
115Z ASN* 1.3 83.7 - - - +
117Z ALA* 1.3 61.4 + - - +
119Z THR* 2.6 21.3 + - - +
120Z THR* 2.8 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037 ALA* 3.2 39.1 - - + +
1067 THR* 4.9 7.6 - - + -
1077 GLU* 3.8 20.0 - - + +
7U PRO 5.8 1.8 + - - +
8U LYS* 5.1 3.1 - - + -
113Z LEU 5.2 1.6 + - - +
114Z GLN 5.1 0.8 + - - -
115Z ASN 3.6 0.2 - - - -
116Z VAL* 1.3 79.3 - - - +
118Z GLU* 1.3 57.3 + - - +
120Z THR* 3.5 11.7 - - + +
121Z LYS* 3.0 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077 GLU* 3.8 24.6 + - - +
115Z ASN* 3.8 24.9 - - - +
117Z ALA* 1.3 78.3 - - - +
119Z THR* 1.3 59.9 + - + +
121Z LYS* 3.3 37.5 + - - +
122Z VAL* 3.5 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107 LEU* 3.8 19.0 - - + +
147 LYS* 2.5 32.2 + - - -
115Z ASN* 3.3 20.2 + - + +
116Z VAL* 2.6 13.9 + - - +
118Z GLU* 1.3 81.3 - - + +
120Z THR* 1.3 60.1 + - - +
121Z LYS 3.2 0.7 - - - -
122Z VAL* 3.1 9.2 + - - +
123Z LEU* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147 LYS* 3.2 17.0 - - - +
7U PRO* 3.4 28.1 - - + +
8U LYS* 3.7 27.7 + - + -
116Z VAL 2.8 20.8 + - - +
117Z ALA* 3.5 14.4 - - + +
119Z THR* 1.3 69.7 - - - +
121Z LYS* 1.3 58.6 + - - +
122Z VAL 3.1 5.4 - - - -
123Z LEU* 3.5 21.2 - - - +
124Z PHE* 3.3 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997 ALA* 6.4 0.4 - - - -
1007 MET* 4.9 16.8 - - + -
1037 ALA* 4.7 13.2 - - + -
1047 LYS* 3.9 31.2 - - + +
1077 GLU* 4.9 2.5 - - - +
8U LYS* 4.8 4.0 - - - +
117Z ALA 3.0 15.0 + - - +
118Z GLU* 3.3 39.2 + - - +
120Z THR* 1.3 76.8 - - - +
122Z VAL* 1.3 64.7 + - + +
124Z PHE* 4.5 6.7 - - - -
125Z ASP* 3.1 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107 LEU* 4.8 11.2 - - + -
118Z GLU 3.5 19.3 - - - +
119Z THR* 3.1 8.4 + - - +
121Z LYS* 1.3 89.9 - - + +
123Z LEU* 1.3 62.2 + - - +
124Z PHE 3.3 1.1 - - - -
125Z ASP* 3.4 4.4 + - - +
126Z VAL* 2.9 52.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77 ALA 5.7 0.4 - - - +
107 LEU* 3.7 19.6 - - + +
117 ASP* 4.3 21.5 - - + +
147 LYS* 3.7 37.0 - - + -
277 THR* 5.6 10.5 - - + -
7U PRO* 5.7 1.3 - - + -
119Z THR 2.9 15.9 + - - +
120Z THR* 3.5 23.3 - - - +
122Z VAL* 1.3 75.2 - - - +
124Z PHE* 1.3 51.9 + - - +
126Z VAL* 5.2 1.1 - - - -
127Z SER* 2.6 51.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957 PHE* 3.7 28.3 - + + -
967 GLU* 3.6 27.1 - - + -
997 ALA* 3.9 20.2 - - + -
3U THR* 3.1 38.3 - - - +
4U LEU 5.6 2.2 - - - -
5U ILE* 4.9 10.8 - - + -
8U LYS* 5.1 2.2 - - - -
120Z THR* 3.3 18.7 + - - +
121Z LYS* 4.6 5.6 - - - -
123Z LEU* 1.3 80.0 - - - +
125Z ASP* 1.3 70.1 + - - +
127Z SER* 2.8 19.4 + - - -
128Z LYS* 3.0 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967 GLU* 3.8 13.7 - - - +
121Z LYS 3.1 19.8 - - - +
122Z VAL* 3.4 7.4 + - - +
123Z LEU 3.4 0.2 - - - -
124Z PHE* 1.3 87.2 - - - +
126Z VAL* 1.3 63.5 + - + +
128Z LYS* 3.2 30.3 + - - +
129Z GLU* 2.9 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67 ALA* 5.4 1.3 - - + -
77 ALA* 3.6 31.9 - - + +
122Z VAL* 2.9 32.0 + - + +
123Z LEU* 4.5 1.6 - - - +
125Z ASP* 1.3 80.3 - - + +
127Z SER* 1.3 57.8 + - - +
129Z GLU* 3.4 15.9 + - - +
130Z THR* 2.9 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 127 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77 ALA* 5.7 1.6 - - - -
117 ASP* 6.5 0.2 - - - -
347 LYS* 4.3 17.8 - - - +
3U THR* 4.0 10.5 - - - +
123Z LEU* 2.6 36.7 + - - +
124Z PHE* 2.8 15.6 + - - -
126Z VAL* 1.3 78.3 - - - +
128Z LYS* 1.3 55.4 + - - +
130Z THR* 2.7 22.0 + - - -
131Z VAL* 2.9 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927 ILE* 3.4 40.7 - - + +
957 PHE* 6.3 0.4 - - + -
967 GLU* 4.6 6.1 - - - +
3U THR* 4.0 15.5 - - + +
124Z PHE* 3.0 32.2 + - + +
125Z ASP* 3.2 41.5 + - - +
127Z SER* 1.3 80.9 + - - +
129Z GLU* 1.3 66.3 + - - +
131Z VAL* 3.5 9.5 - - - +
132Z GLU* 2.9 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927 ILE* 6.3 0.2 - - + -
125Z ASP* 2.9 27.8 + - - +
126Z VAL* 3.6 18.0 - - + +
127Z SER 3.2 0.2 - - - -
128Z LYS* 1.3 88.7 + - - +
130Z THR* 1.3 58.4 + - + +
132Z GLU* 4.5 1.3 - - - +
133Z LEU* 2.9 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47 LYS* 5.2 14.6 - - + -
77 ALA* 3.8 23.0 - - + +
347 LYS* 3.7 20.5 + - - +
377 ASP* 4.8 1.2 - - - +
387 GLU* 4.8 12.7 - - - +
126Z VAL* 2.9 20.0 + - + +
127Z SER* 2.7 24.1 + - - -
129Z GLU* 1.3 73.4 - - + +
131Z VAL* 1.3 66.3 + - - +
133Z LEU* 5.2 1.8 - - - -
134Z GLU* 3.7 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307 SER* 4.8 6.1 - - - +
337 LYS* 5.9 4.9 - - + -
347 LYS* 3.6 28.9 - - + +
377 ASP* 3.3 26.9 - - - +
1U VAL 5.3 8.5 - - - +
3U THR* 6.1 2.0 - - + -
127Z SER* 2.9 21.2 + - - +
128Z LYS* 3.5 11.7 - - - +
129Z GLU 3.2 0.2 - - - -
130Z THR* 1.3 79.8 - - - +
132Z GLU* 1.3 75.4 + - + +
133Z LEU 3.6 0.7 + - - -
134Z GLU* 3.8 8.5 + - - +
135Z SER 5.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696 GLU* 3.3 20.7 - - - +
857 ALA 5.1 5.7 - - - +
887 GLN* 2.6 44.9 + - - +
927 ILE* 3.5 13.0 - - - +
1U VAL 5.0 6.2 - - - +
2U SER* 6.0 0.5 - - - -
128Z LYS* 2.9 22.6 + - - +
129Z GLU* 3.8 1.1 - - - -
131Z VAL* 1.3 90.6 - - + +
133Z LEU* 1.3 62.9 + - - +
134Z GLU 3.2 6.3 + - - -
135Z SER* 4.4 10.9 + - - +
136Z GLU* 3.8 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867 SER* 6.0 4.9 - - - +
129Z GLU* 2.9 37.8 + - + +
130Z THR* 4.4 2.7 - - - -
131Z VAL 3.4 0.8 - - - -
132Z GLU* 1.3 81.7 - - - +
134Z GLU* 1.3 65.1 + - + +
136Z GLU* 3.0 37.0 - - - +
----------------------------------------------------------
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