Contacts of the helix formed by residues 13 - 32 (chain C) in PDB entry 4STD
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 PHE 13 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 3.5 38.0 - + + -
10B GLU* 5.9 0.2 - - - -
11B ILE* 3.5 15.9 - - + -
12B THR* 3.4 7.2 - - - -
13B PHE* 3.2 53.8 - + + -
16B TYR* 3.7 20.2 - + + -
12C THR* 1.3 79.3 - - + +
14C SER* 1.3 61.2 + - - +
16C TYR* 3.2 23.2 + + - +
17C LEU* 3.0 46.0 + - + +
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Residues in contact with SER 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 2.8 35.7 + - - +
12C THR* 3.2 10.0 - - - +
13C PHE* 1.3 76.5 - - - +
15C ASP* 1.3 63.4 - - - +
17C LEU* 3.3 5.9 + - - +
18C GLY* 2.9 25.5 + - - -
142C TRP* 5.2 0.2 - - - -
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Residues in contact with ASP 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 4.0 13.7 - - + +
12C THR* 3.2 36.0 + - - +
14C SER* 1.3 81.6 - - - +
16C TYR* 1.3 51.2 - - - +
18C GLY* 3.2 1.7 + - - -
19C LEU* 2.7 43.2 + - + +
94C LYS* 4.4 9.5 + - - -
137C LYS* 4.1 11.8 - - - +
142C TRP* 3.2 39.4 + - + +
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Residues in contact with TYR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 3.8 17.0 - + + -
16A TYR* 2.8 29.5 + + - -
20A MET* 3.7 13.8 - - + -
16B TYR* 3.1 31.7 + + - -
11C ILE* 4.2 11.2 - - + +
12C THR 3.1 9.4 + - - +
13C PHE* 3.2 28.9 - + - +
15C ASP* 1.3 79.7 - - - +
17C LEU* 1.3 56.0 + - - +
19C LEU* 3.1 4.3 + - - +
20C MET* 2.9 58.4 + - + +
92C TRP* 3.1 41.7 + + - -
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 4.0 26.9 - - + +
11B ILE* 3.7 33.9 - - + +
16B TYR* 5.1 1.1 - - + -
92B TRP* 4.8 8.6 + - + +
13C PHE* 3.0 53.9 + - + +
14C SER* 3.6 6.3 - - - +
16C TYR* 1.3 75.0 - - - +
18C GLY* 1.3 60.0 + - - +
20C MET* 3.6 26.9 + - + +
21C THR* 2.9 28.4 + - - -
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Residues in contact with GLY 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C SER 2.9 14.3 + - - -
15C ASP 3.5 3.4 - - - -
17C LEU* 1.3 76.9 - - - +
19C LEU* 1.3 58.5 + - - +
21C THR* 3.7 7.0 + - - +
22C CYS* 3.3 25.5 + - - +
142C TRP* 4.0 18.0 + - - +
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 4.0 19.1 - - + -
15C ASP* 2.7 36.6 + - + +
16C TYR* 3.1 5.1 + - - +
18C GLY* 1.3 71.8 - - - +
20C MET* 1.3 64.1 + - - +
22C CYS* 3.8 4.6 - - - +
23C VAL* 3.2 25.1 + - - +
92C TRP* 3.7 27.1 - - + -
100C VAL* 3.9 27.8 - - + -
135C TYR* 3.6 40.7 - - + -
142C TRP* 3.8 21.8 - - + -
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Residues in contact with MET 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 4.0 10.5 - - + -
90B THR* 3.7 23.1 - - - +
91B ARG* 5.1 1.6 - - - -
92B TRP* 3.9 22.0 - - + +
16C TYR* 2.9 51.9 + - + +
17C LEU* 3.6 38.6 - - + +
19C LEU* 1.3 74.7 - - - +
21C THR* 1.3 61.9 + - - +
23C VAL* 3.5 9.7 - - + +
24C TYR* 2.9 32.2 + - - +
92C TRP* 4.9 5.8 - - + -
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Residues in contact with THR 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 3.4 37.3 - - - +
92B TRP 4.9 5.4 + - - -
17C LEU 2.9 17.3 + - - -
18C GLY* 3.7 8.2 - - - -
20C MET* 1.3 77.4 - - - +
22C CYS* 1.3 57.1 + - - +
24C TYR* 3.7 1.0 - - - +
25C GLU* 3.0 42.9 + - + +
41C VAL* 5.7 2.0 - - + -
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Residues in contact with CYS 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLY 3.3 15.5 + - - +
19C LEU* 3.8 7.6 - - - +
20C MET 3.3 0.2 - - - -
21C THR* 1.3 81.1 - - - +
23C VAL* 1.3 56.6 + - - +
25C GLU* 3.6 2.3 + - - +
26C TRP* 3.1 27.9 + - - +
41C VAL* 3.7 22.0 - - + +
135C TYR* 3.7 17.9 - - + -
142C TRP* 3.8 13.5 - - + +
143C LYS* 3.6 7.6 - - - -
144C PHE* 3.2 34.5 - - - -
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Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLY* 6.3 0.7 - - - -
19C LEU 3.2 11.5 + - - +
20C MET* 3.5 15.7 - - + +
22C CYS* 1.3 77.0 - - - +
24C TYR* 1.3 67.3 + - + +
26C TRP* 3.5 9.7 + - + +
27C ALA* 3.1 21.1 + - - +
87C ILE* 3.7 22.2 - - + +
92C TRP* 4.6 3.4 - - + -
104C HIS* 3.8 21.1 - - + +
133C HIS* 3.8 19.7 - - + +
135C TYR* 3.2 29.6 - - + +
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Residues in contact with TYR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLY* 3.4 33.7 - - - -
90B THR* 3.9 9.4 - - - +
91B ARG* 3.6 30.1 - - + -
103B TYR* 3.5 38.0 - + + +
104B HIS 4.2 2.9 + - - -
105B GLN* 3.7 18.9 + - + +
130B ALA* 4.0 16.6 - - - +
20C MET 2.9 19.8 + - - +
21C THR 3.7 2.7 - - - +
23C VAL* 1.3 78.1 - - + +
25C GLU* 1.3 57.2 + - - +
27C ALA* 3.3 3.1 + - - +
28C ASP* 2.8 48.8 + - + +
37C ARG* 3.6 21.5 + - - -
87C ILE* 4.4 8.1 - - - -
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 2.5 34.1 + - - +
21C THR* 3.0 28.8 + - + +
22C CYS 3.8 0.7 - - - +
24C TYR* 1.3 73.4 - - - +
26C TRP* 1.3 60.6 + - - +
28C ASP 4.6 0.2 - - - +
29C SER* 2.9 36.0 + - - +
37C ARG* 2.9 47.9 + - - +
40C LYS* 5.9 2.6 - - - +
41C VAL* 3.6 30.9 - - + +
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Residues in contact with TRP 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C CYS 3.1 18.2 + - - +
23C VAL* 3.5 14.6 - - + +
25C GLU* 1.3 76.2 - - - +
27C ALA* 1.3 94.9 - - + +
29C SER* 3.0 19.1 + - - -
30C TYR* 3.1 59.8 + + - -
38C LEU* 4.1 13.2 - - + -
41C VAL* 4.2 4.9 - - + +
85C HIS* 4.4 11.4 - + + -
87C ILE* 4.9 1.1 - - + -
106C LEU* 3.9 30.5 - - + -
133C HIS* 3.7 25.6 - + - -
144C PHE* 3.4 43.2 - + + -
147C LEU* 3.8 21.1 - - + -
175C BFS 4.3 4.5 - - - -
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Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLN* 3.5 10.3 - - - +
23C VAL 3.1 10.0 + - - +
24C TYR 3.7 2.0 - - - +
26C TRP* 1.3 103.9 - - + +
28C ASP* 1.3 61.1 + - - +
30C TYR* 3.2 19.7 + - - +
31C ASP* 3.3 14.4 + - - +
85C HIS* 3.3 29.3 - - - +
87C ILE* 3.9 7.2 - - + -
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Residues in contact with ASP 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLN* 4.5 7.8 + - - +
130B ALA* 4.1 5.6 - - - +
152B ARG* 2.9 39.5 + - - -
24C TYR* 2.8 40.9 + - + +
27C ALA* 1.3 71.2 - - - +
29C SER* 1.3 60.2 + - - +
31C ASP* 3.8 8.0 - - - +
32C SER* 2.9 34.5 + - - -
37C ARG* 2.7 36.0 + - - +
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Residues in contact with SER 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLU 2.9 17.5 + - - -
26C TRP 3.0 11.3 + - - -
28C ASP* 1.3 73.2 - - - +
30C TYR* 1.3 64.9 + - - +
32C SER* 4.3 2.5 - - - -
33C LYS* 2.9 24.6 + - - -
34C ASP* 3.0 28.4 + - - -
35C TRP* 4.0 3.9 - - - -
37C ARG* 3.9 14.7 - - - +
38C LEU* 3.3 33.0 - - - +
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Residues in contact with TYR 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 3.1 53.3 + + - -
27C ALA 3.2 11.4 + - - +
28C ASP 3.2 0.2 - - - -
29C SER* 1.3 88.2 + - - +
31C ASP* 1.3 60.3 + - - +
33C LYS* 3.4 18.5 + - - +
35C TRP* 4.2 8.1 - + - -
38C LEU* 3.8 27.8 - - + -
50C TYR* 4.9 1.9 + - - -
66C PHE* 3.3 20.6 - - - -
70C VAL* 3.8 13.9 - - + +
76C LEU* 3.6 36.5 - - + +
83C THR* 4.4 1.9 + - - -
85C HIS* 3.6 25.4 - + - +
147C LEU* 4.7 5.0 - - - +
175C BFS 3.6 23.9 + - + +
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Residues in contact with ASP 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLN* 4.3 6.2 + - - -
152B ARG* 4.1 22.2 + - + +
27C ALA 3.3 13.8 + - - +
28C ASP* 3.9 9.8 - - - +
29C SER 3.3 0.2 - - - -
30C TYR* 1.3 74.1 - - - +
32C SER* 1.3 60.8 + - - +
33C LYS* 3.2 11.4 + - - +
82C ARG* 4.7 13.9 + - - -
83C THR* 2.9 32.8 + - - +
84C GLN* 3.3 19.2 - - - +
85C HIS* 3.1 31.5 + - - -
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Residues in contact with SER 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ARG* 2.9 31.3 + - - +
28C ASP 2.9 17.7 + - - -
31C ASP* 1.3 75.2 - - - +
33C LYS* 1.3 69.6 + - - +
34C ASP* 3.2 21.3 + - - +
37C ARG* 3.4 9.9 + - - -
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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
------------------------------------------------------------
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