Contacts of the helix formed by residues 11 - 27 (chain C) in PDB entry 2XVF
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 GLY 11 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLY 3.6 2.6 - - - -
10C ALA* 1.3 79.1 - - - +
12C PRO* 1.3 77.7 - - - +
13C SER 3.1 3.7 + - - -
14C GLY 3.2 2.2 + - - +
15C MSE 3.0 26.7 + - - +
38C GLU* 4.2 1.2 + - - -
44C GLY 3.7 0.2 - - - -
45C GLY* 3.4 19.6 - - - +
161C CYS 5.1 4.4 + - - -
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Residues in contact with PRO 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLY* 1.3 81.9 - - - +
13C SER* 1.3 57.7 + - - +
15C MSE 3.7 10.2 - - - +
16C ALA* 3.0 27.0 + - - +
44C GLY 3.4 15.0 - - - +
45C GLY* 4.4 2.5 - - - -
46C GLN* 4.8 2.2 - - + +
47C TRP* 3.7 28.7 - - + +
81C PHE* 5.9 3.3 - - + -
107C ILE* 4.0 11.4 - - + -
110C ARG* 5.0 2.3 + - - -
322C PHE* 3.8 23.1 - - + -
325C PHE* 3.9 18.2 - - + +
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Residues in contact with SER 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLY 3.2 0.6 - - - -
12C PRO* 1.3 78.4 - - - +
14C GLY* 1.3 59.9 + - - +
16C ALA* 3.1 5.2 + - - +
17C GLN* 2.9 26.5 + - - +
161C CYS* 3.8 20.9 - - - -
313C ILE* 3.0 40.4 + - - +
314C GLY* 4.1 1.4 - - - -
325C PHE* 3.5 24.7 - - - -
329C ALA* 4.9 0.2 - - - +
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Residues in contact with GLY 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 4.0 9.5 - - - +
9C GLY 3.2 26.2 + - - -
10C ALA* 4.7 1.3 - - - -
11C GLY 3.2 6.0 + - - +
13C SER* 1.3 75.0 - - - +
15C MSE 1.3 64.7 + - - +
17C GLN* 3.2 4.0 + - - +
18C LEU* 3.0 31.1 + - - +
161C CYS* 3.8 11.9 - - - +
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Residues in contact with MSE 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ALA* 3.8 12.8 - - + +
11C GLY 3.0 30.4 + - - +
12C PRO* 3.7 10.3 - - + +
14C GLY* 1.3 74.2 - - - +
16C ALA* 1.3 51.8 + - - +
18C LEU* 3.2 11.5 + - + +
19C ARG* 2.7 37.8 + - - +
43C TRP* 3.6 35.0 - - + -
44C GLY* 3.7 16.8 - - - +
107C ILE* 4.2 15.3 - - + +
108C LYS* 3.8 31.6 - - + +
110C ARG* 4.8 1.8 - - - +
111C VAL* 3.5 27.5 - - + +
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Residues in contact with ALA 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PRO 3.0 16.5 + - - +
13C SER* 3.1 11.2 + - - +
15C MSE 1.3 74.6 - - - +
17C GLN* 1.3 54.5 + - - +
19C ARG* 3.6 1.3 - - - +
20C ALA* 2.7 36.4 + - - +
110C ARG* 3.7 12.9 - - - +
325C PHE* 4.1 3.6 - - + -
326C ASP* 3.4 31.9 - - - +
329C ALA* 3.7 15.9 - - + +
330C TRP* 4.3 2.0 - - - -
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Residues in contact with GLN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.8 29.2 - - + -
13C SER 2.9 12.1 + - - +
14C GLY* 3.2 8.5 + - - +
16C ALA* 1.3 76.0 - - - +
18C LEU* 1.3 62.2 + - - +
20C ALA* 3.5 0.5 + - - +
21C PHE* 3.2 46.5 + - + -
159C VAL* 3.6 21.2 - - + +
161C CYS* 4.7 2.0 - - - -
313C ILE* 3.5 24.9 - - - +
329C ALA* 3.2 41.0 + - - +
332C ALA* 3.9 5.1 - - - +
333C ARG* 3.9 5.5 + - - +
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.9 21.5 - - + -
14C GLY 3.0 19.8 + - - +
15C MSE 3.5 8.7 - - - +
17C GLN* 1.3 72.8 - - - +
19C ARG* 1.3 65.7 + - - +
21C PHE* 3.0 8.8 + - - +
22C GLN* 2.9 21.1 + - - +
34C LEU* 4.1 10.6 - - + +
36C CYS* 4.1 11.9 - - + -
111C VAL* 5.7 0.7 - - + -
116C VAL* 3.8 26.5 - - + +
119C TYR* 3.8 34.3 - - + -
120C ILE* 3.8 35.2 - - + -
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Residues in contact with ARG 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C MSE 2.7 21.1 + - - +
16C ALA* 3.6 7.6 - - - +
18C LEU* 1.3 71.7 - - - +
20C ALA* 1.3 58.2 + - - +
22C GLN* 2.6 40.5 + - - +
23C SER* 2.8 39.0 + - - -
83C ASP* 2.8 40.4 + - - +
84C TYR* 4.9 3.0 - - - +
110C ARG* 3.8 48.6 + - + +
111C VAL* 5.0 4.9 - - + -
113C LYS* 4.7 18.5 - - - +
114C ALA* 3.7 19.6 - - + +
116C VAL* 4.5 3.5 - - - +
330C TRP* 4.0 8.1 - - + -
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Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA 2.7 20.5 + - - +
17C GLN 3.6 5.2 - - - +
19C ARG* 1.3 71.1 - - - +
21C PHE* 1.3 63.2 + - - +
23C SER 3.2 1.0 + - - -
24C ALA 3.1 9.0 + - - -
329C ALA* 3.9 20.4 - - + +
330C TRP* 3.6 33.8 - - + -
333C ARG* 2.8 32.9 + - + +
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Residues in contact with PHE 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 4.5 9.9 - - + -
7C ILE* 4.8 1.6 - - + -
17C GLN* 3.2 44.9 + - + -
18C LEU 3.0 7.8 + - - +
20C ALA* 1.3 79.6 - - - +
22C GLN* 1.3 60.4 + - - +
24C ALA* 3.3 2.4 + - - +
25C GLN* 3.1 17.7 + - - +
31C ILE* 3.4 22.3 - - + +
32C PRO* 3.7 33.4 - - + -
34C LEU* 3.7 35.9 - - + -
333C ARG* 3.7 33.0 - - + +
336C ILE* 4.1 22.4 - - + -
337C MSE 4.1 11.9 - - + -
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Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU 2.9 6.3 + - - -
19C ARG* 2.6 51.2 - - - +
21C PHE* 1.3 76.9 - - - +
23C SER* 1.3 67.7 + - - +
25C GLN* 3.4 16.9 + - - +
26C GLU* 2.8 38.8 + - - +
31C ILE* 4.7 2.0 - - - +
34C LEU* 5.5 0.6 - - - +
114C ALA* 3.6 35.2 - - + +
116C VAL* 3.6 22.7 - - + -
119C TYR* 5.6 2.5 - - + -
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ARG* 2.8 32.9 + - - -
20C ALA 3.6 5.2 - - - -
21C PHE 3.2 0.4 - - - -
22C GLN* 1.3 88.2 + - - +
24C ALA* 1.3 64.8 + - - +
26C GLU* 3.5 5.1 + - - +
27C LYS* 3.3 36.8 + - - +
83C ASP* 4.3 1.2 + - - -
330C TRP* 3.7 22.5 - - - -
333C ARG* 4.3 2.7 - - - -
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA 3.1 12.1 + - - +
21C PHE 3.6 8.3 - - - +
23C SER* 1.3 77.0 - - - +
25C GLN* 1.3 58.6 + - - +
27C LYS* 3.4 9.3 + - - +
28C GLY 3.3 5.7 + - - -
29C ALA* 3.2 22.6 + - - +
31C ILE* 4.1 4.5 - - + -
333C ARG* 3.8 14.0 - - - +
337C MSE 4.1 13.2 - - + -
339C ARG* 3.9 29.2 + - - +
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Residues in contact with GLN 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PHE 3.1 14.4 + - - +
22C GLN* 3.8 14.2 + - - +
24C ALA* 1.3 72.7 - - - +
26C GLU* 1.3 56.6 + - - +
27C LYS 3.0 4.9 - - - -
28C GLY* 2.9 19.9 + - - -
29C ALA 3.6 16.1 + - - +
31C ILE* 3.8 33.6 + - + +
118C LYS* 6.0 0.6 - - - +
119C TYR* 4.0 13.7 + - - -
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 2.8 32.9 + - - +
23C SER* 3.9 7.4 - - - +
24C ALA 3.5 0.2 - - - -
25C GLN* 1.3 73.4 - - - +
27C LYS* 1.3 61.6 + - + +
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Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C SER* 3.3 24.0 + - - +
24C ALA* 3.8 8.3 - - - +
25C GLN 3.0 1.0 - - - -
26C GLU* 1.3 80.1 - - + +
28C GLY* 1.3 56.8 + - - +
29C ALA 3.8 0.4 - - - -
330C TRP* 6.1 0.8 - - - +
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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
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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) + - + + + + + -
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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