Contacts of the helix formed by residues 41 - 58 (chain C) in PDB entry 2VE7
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 41 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASN* 3.2 32.1 + - - +
35C ASP* 3.1 33.4 + - + +
39C ASN 3.7 5.8 - - - +
40C PRO* 1.3 75.1 - - - +
42C PRO* 1.3 71.1 - - + +
43C GLU* 3.1 4.0 - - + +
44C VAL* 2.8 30.7 + - + +
45C LEU* 3.0 12.4 + - - +
112C PRO* 4.6 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP* 5.7 2.9 - - - +
40C PRO 3.5 9.0 - - - +
41C LYS* 1.3 83.7 - - + -
43C GLU* 1.3 59.9 + - + +
45C LEU* 3.4 2.4 + - + -
46C HIS* 2.3 57.4 + - + +
110C LEU 4.3 10.8 - - - +
111C CYS* 5.3 0.2 - - - -
112C PRO* 3.8 28.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LYS* 3.0 3.8 + - + -
42C PRO* 1.3 80.9 - - + +
44C VAL* 1.3 64.2 + - + +
46C HIS* 3.5 10.8 - - + +
47C MET* 3.2 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 5.2 4.0 - - + -
31C LEU* 3.9 28.0 - - + -
35C ASP* 3.8 37.2 - - + +
36C LEU* 5.0 1.6 - - + -
41C LYS* 2.8 17.4 + - + +
43C GLU* 1.3 75.3 - - + +
45C LEU* 1.3 65.3 + - + +
47C MET* 2.9 28.4 + - + +
48C ILE* 3.0 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ASP 5.7 0.2 - - - +
36C LEU* 4.8 7.4 - - + -
40C PRO* 3.6 20.0 - - + -
41C LYS 3.0 10.0 + - - +
42C PRO* 3.9 7.0 - - + +
44C VAL* 1.3 75.8 - - + +
46C HIS* 1.3 59.5 + - + +
48C ILE* 3.2 8.2 + - + +
49C TYR* 2.9 71.7 + - + +
112C PRO* 3.2 37.0 - - + -
117C THR* 3.9 13.2 - - + +
121C LEU* 4.1 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP 5.7 2.0 + - - -
42C PRO* 2.3 48.2 + - + +
43C GLU* 3.5 12.3 - - + +
45C LEU* 1.3 77.7 - - + +
47C MET* 1.3 62.3 - - - +
49C TYR* 3.9 2.1 - - - +
50C MET* 3.0 44.3 + - + +
84C PRO* 4.4 22.2 - - + -
85C PHE* 5.2 4.6 + - - +
88C LEU* 4.2 13.7 - - + +
109C ILE* 3.1 39.1 + - + +
110C LEU* 5.2 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 4.1 16.8 - - + -
27C ASP* 3.0 44.2 - - - +
43C GLU* 3.2 13.9 + - + +
44C VAL* 2.9 21.1 + - + +
46C HIS* 1.3 79.4 - - - +
48C ILE* 1.3 58.0 + - + +
50C MET* 3.4 7.6 + - - +
51C ARG* 3.0 36.9 + - + +
61C LEU* 6.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE* 3.7 30.3 - - + -
22C ILE* 3.8 24.5 - - + +
23C LEU* 4.2 22.9 - - + -
31C LEU* 4.8 1.3 - - + -
36C LEU* 4.8 9.2 - - + -
44C VAL* 3.0 30.7 + - + +
45C LEU* 3.2 10.3 + - + +
47C MET* 1.3 75.5 - - - +
49C TYR* 1.3 58.8 + - + +
51C ARG* 3.2 4.2 + - - +
52C ALA* 2.9 29.1 + - + +
121C LEU* 3.9 31.2 - - + -
124C ILE* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 2.9 63.0 + - + +
46C HIS* 4.0 7.4 - - - +
48C ILE* 1.3 72.3 - - - +
50C MET* 1.3 56.9 + - - +
52C ALA* 3.3 4.9 + - - +
53C LEU* 2.9 37.9 + - - +
88C LEU* 4.0 18.4 - - + -
92C LEU* 3.9 33.2 - - + +
96C LEU* 5.0 0.7 - - + -
104C PHE* 3.9 25.3 - + - -
108C ASP 4.6 8.4 + - - -
109C ILE* 5.2 5.2 - - + -
117C THR* 4.1 15.6 - - - +
120C PHE* 4.1 9.1 - - + +
121C LEU* 4.4 6.5 - - + +
124C ILE* 3.8 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C HIS* 3.0 46.9 + - + +
47C MET* 3.6 6.3 - - - +
49C TYR* 1.3 73.8 - - - +
51C ARG* 1.3 60.6 + - + +
53C LEU* 3.4 3.2 + - - +
54C GLN* 2.9 30.7 + - - +
61C LEU* 5.5 10.8 - - + +
64C PHE* 3.5 56.1 - - + -
65C TYR* 4.3 18.8 - - - +
84C PRO* 3.8 25.4 - - + -
88C LEU* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLU* 3.3 33.1 + - - -
21C LYS 5.4 0.2 + - - -
22C ILE* 2.7 50.0 + - + +
23C LEU* 3.7 14.8 - - + -
24C THR* 3.5 31.9 + - - +
27C ASP* 6.1 0.9 - - - -
47C MET* 3.0 20.3 + - + +
48C ILE 3.2 2.9 + - - +
50C MET* 1.3 73.2 - - + +
52C ALA* 1.3 66.1 + - - +
54C GLN* 3.2 21.7 + - - +
55C ILE* 2.9 45.4 + - - +
61C LEU* 6.1 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 4.1 11.6 - - + +
48C ILE* 2.9 17.4 + - + +
49C TYR* 3.6 7.9 - - - +
51C ARG* 1.3 74.9 - - - +
53C LEU* 1.3 58.9 + - - +
55C ILE* 3.1 8.5 + - - +
56C VAL* 2.8 36.0 + - - +
95C PHE* 4.1 12.6 - - + -
124C ILE* 4.0 29.6 - - + -
128C ILE* 4.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C TYR 2.9 22.1 + - - +
50C MET 3.6 3.8 - - - +
52C ALA* 1.3 76.6 - - - +
54C GLN* 1.3 56.1 + - - +
56C VAL* 4.5 1.3 - - - +
57C TYR* 2.8 68.7 + - + +
58C GLY 3.5 0.2 + - - -
59C ILE* 4.3 6.4 + - + -
64C PHE* 3.9 25.1 - - + -
88C LEU* 4.0 17.0 - - + +
91C HIS* 3.8 27.1 - - + -
92C LEU* 4.5 10.3 - - + +
95C PHE* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A THR* 4.6 1.0 + - - -
216A GLU* 3.7 23.9 + - - +
50C MET 2.9 19.1 + - - +
51C ARG* 3.2 27.1 + - - +
53C LEU* 1.3 75.4 - - - +
55C ILE* 1.3 59.0 + - - +
58C GLY* 2.9 25.3 + - - -
59C ILE* 3.0 34.2 + - - +
60C ARG* 5.1 3.0 - - - +
61C LEU* 4.4 19.0 + - - +
64C PHE* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A THR* 3.3 20.3 + - - -
216A GLU* 4.0 16.2 - - - +
217A ASP* 4.3 9.3 - - - +
21C LYS 3.2 26.5 - - - +
22C ILE* 3.9 15.9 - - + +
51C ARG* 2.9 45.3 + - - +
52C ALA* 3.5 6.7 - - - +
54C GLN* 1.3 77.3 - - - +
56C VAL* 1.3 68.7 + - + +
128C ILE* 5.0 14.6 - - + -
131C ARG* 3.4 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ASN* 3.1 18.0 + - - -
226A LEU* 3.7 25.9 - - + +
52C ALA 2.8 24.3 + - - +
53C LEU 4.3 0.7 - - - +
55C ILE* 1.3 75.5 - - + +
57C TYR* 1.3 64.7 + - + +
95C PHE* 3.5 36.8 - - + -
98C ILE* 6.2 0.7 - - + -
127C PHE* 3.7 31.0 - - + -
128C ILE* 4.8 12.3 - - + -
131C ARG* 3.6 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLY* 3.2 25.6 + - - +
222A ASN* 3.6 6.9 + - - +
226A LEU* 3.4 28.7 - - + -
230A ILE* 6.2 0.7 - - + -
53C LEU* 2.8 51.7 + - + +
56C VAL* 1.3 78.2 - - + +
58C GLY* 1.3 61.9 + - - +
59C ILE* 4.0 20.8 - - + +
91C HIS* 4.7 12.8 - + + -
94C SER* 3.3 22.4 + - - -
95C PHE* 3.5 29.8 - + + +
98C ILE* 3.8 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLY* 3.4 17.2 - - - -
214A GLU 4.0 17.9 - - - +
215A THR* 4.4 6.3 - - - -
216A GLU 5.9 0.2 - - - -
53C LEU 3.5 0.4 + - - -
54C GLN* 2.9 19.8 + - - -
55C ILE 4.1 1.2 + - - -
56C VAL 3.7 1.0 - - - -
57C TYR* 1.3 83.7 - - - +
59C ILE* 1.3 61.8 + - - +
60C ARG* 5.8 3.6 + - - -
----------------------------------------------------------
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