Contacts of the helix formed by residues 10 - 29 (chain C) in PDB entry 5YL4
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 10 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 1.3 75.2 - - - +
11C GLN* 1.3 60.7 + - - -
12C ALA 3.4 1.3 - - - -
14C VAL* 2.8 31.6 + - - +
68C VAL 2.9 11.9 + - - -
69C ASP* 3.5 23.8 - - - -
145C THR* 4.0 5.7 - - - +
501C GTP 3.5 16.2 - - - -
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Residues in contact with GLN 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLY* 1.3 71.9 - - - +
12C ALA* 1.3 58.7 + - - +
14C VAL* 3.6 0.7 - - - +
15C GLN* 2.9 49.0 + - - +
69C ASP* 3.6 6.9 + - - -
71C GLU* 5.1 2.1 - - - +
74C VAL* 3.8 32.3 - - + +
224C TYR* 3.7 5.7 - - - -
501C GTP 3.0 57.2 + - - +
502C MG 4.2 1.8 - - - -
245D GLN* 2.7 35.4 + - - +
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Residues in contact with ALA 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLN* 1.3 77.3 - - - +
13C GLY* 1.3 58.6 + - - +
15C GLN* 4.3 0.2 - - - +
16C ILE* 2.9 42.7 + - + +
140C SER* 3.8 19.1 - - - +
171C ILE* 4.8 3.1 - - + -
501C GTP 3.2 57.7 + - + +
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Residues in contact with GLY 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C HIS* 3.2 17.3 + - - -
9C VAL 3.5 10.2 + - - -
10C GLY 3.4 1.8 + - - -
11C GLN 3.3 0.2 - - - -
12C ALA* 1.3 79.0 - - - +
14C VAL* 1.3 62.1 + - - +
16C ILE* 3.9 3.0 - - - +
17C GLY 2.9 17.8 + - - -
138C PHE* 3.4 34.0 - - - +
139C HIS* 4.1 3.6 - - - +
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Residues in contact with VAL 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C HIS* 4.0 14.1 - - - +
9C VAL 4.3 0.2 + - - -
10C GLY 2.8 27.0 + - - +
11C GLN* 3.6 3.4 - - - +
13C GLY* 1.3 71.8 - - - +
15C GLN* 1.3 59.3 + - - +
17C GLY* 3.0 4.7 + - - -
18C ASN* 3.0 34.1 + - - +
67C PHE* 3.6 21.6 - - + -
68C VAL 4.0 14.6 - - - +
69C ASP* 4.6 2.2 - - + +
74C VAL* 3.8 22.2 - - + +
75C ILE* 3.8 29.2 - - + -
78C VAL* 4.2 6.5 - - + -
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Residues in contact with GLN 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLN* 2.9 46.3 + - - +
14C VAL* 1.3 70.0 - - - +
16C ILE* 1.3 65.0 + - - +
18C ASN* 3.4 17.8 + - - +
19C ALA* 3.2 18.7 + - - +
74C VAL* 3.6 22.7 - - + +
77C GLU* 4.9 6.8 - - - +
224C TYR* 4.3 10.1 - - - +
228C ASN* 3.6 19.3 + - - +
501C GTP 2.9 20.3 + - - +
245D GLN* 5.8 1.0 + - - -
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Residues in contact with ILE 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C HIS* 5.0 0.2 - - - -
12C ALA 2.9 23.5 + - - +
13C GLY* 4.0 3.6 - - - +
15C GLN* 1.3 75.9 - - - +
17C GLY* 1.3 56.4 + - - +
19C ALA* 3.2 4.4 + - - +
20C CYS* 2.9 41.6 + - - -
138C PHE* 3.9 23.3 - - + -
169C PHE* 6.1 0.2 - - + -
171C ILE* 3.5 39.0 - - + -
228C ASN* 3.4 29.2 - - + +
231C ILE* 3.8 31.6 - - + -
235C VAL* 4.9 0.2 - - + -
501C GTP 4.1 6.1 - - - +
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Residues in contact with GLY 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C HIS* 3.3 33.9 + - - -
13C GLY 2.9 11.5 + - - -
14C VAL 3.0 5.6 + - - -
16C ILE* 1.3 73.1 - - - +
18C ASN* 1.3 58.7 + - - +
20C CYS* 4.4 1.6 - - - -
21C TRP* 2.8 40.5 + - - +
67C PHE* 4.2 4.7 - - - -
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Residues in contact with ASN 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 3.0 21.1 + - - +
15C GLN* 3.4 21.9 - - - +
16C ILE 3.4 0.2 - - - -
17C GLY* 1.3 74.6 - - - +
19C ALA* 1.3 63.0 + - - +
21C TRP* 5.1 1.6 - - - -
22C GLU* 3.1 31.6 + - - +
67C PHE* 4.2 5.5 - - - -
74C VAL 5.3 1.4 + - - -
77C GLU* 5.9 1.6 - - - +
78C VAL* 3.2 41.8 - - - +
83C TYR* 6.2 0.3 - - - +
87C PHE* 5.4 2.4 - - - -
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Residues in contact with ALA 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLN 3.2 9.3 + - - +
16C ILE 3.2 7.6 + - - +
18C ASN* 1.3 79.6 - - - +
20C CYS* 1.3 58.5 + - - +
22C GLU* 3.8 7.9 - - - +
23C LEU* 3.0 29.8 + - - +
228C ASN* 3.6 36.6 - - + +
229C ARG* 4.4 6.7 - - + +
232C SER* 3.8 8.7 + - - +
363C VAL* 5.0 4.0 - - - +
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Residues in contact with CYS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C HIS* 5.3 1.8 - - + -
16C ILE* 2.9 36.1 + - - +
17C GLY* 3.8 5.8 - - - +
19C ALA* 1.3 77.7 - - - +
21C TRP* 1.3 59.6 + - + +
23C LEU* 3.3 2.8 + - - +
24C TYR* 2.8 52.1 + - + +
138C PHE* 4.2 7.2 - - + -
232C SER* 3.9 20.0 - - - -
235C VAL* 3.8 33.0 - - - -
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Residues in contact with TRP 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER* 3.9 15.9 - - - -
8C HIS* 3.3 23.9 + + - -
17C GLY* 2.8 36.6 + - - +
18C ASN* 4.4 2.0 - - - +
20C CYS* 1.3 70.8 - - + +
22C GLU* 1.3 64.0 + - - +
24C TYR* 3.7 19.8 - + - +
25C CYS* 2.9 31.2 + - - -
52C PHE* 3.2 40.4 - + + -
53C PHE* 3.4 38.1 - + - -
63C PRO* 3.6 23.3 - - + -
64C ARG 3.9 3.4 - - - -
65C ALA* 3.8 21.1 - - + +
67C PHE* 4.0 11.9 - + - -
86C LEU* 4.8 5.8 - - + -
87C PHE* 4.4 16.6 - + + -
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Residues in contact with GLU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ASN* 3.1 22.4 + - - +
19C ALA* 3.8 5.5 - - - +
21C TRP* 1.3 76.2 - - - +
23C LEU* 1.3 61.7 + - - +
25C CYS* 3.4 3.5 + - - +
26C LEU* 3.2 26.9 + - + +
83C TYR* 3.6 45.3 + - + +
229C ARG* 5.6 0.2 + - - -
363C VAL* 3.1 36.0 - - + +
364C PRO* 4.8 4.7 - - - +
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA 3.0 18.3 + - - +
20C CYS 3.5 5.4 - - - +
21C TRP 3.2 0.2 - - - -
22C GLU* 1.3 75.1 - - - +
24C TYR* 1.3 60.3 + - + +
26C LEU* 3.3 4.6 + - + +
27C GLU* 3.0 42.6 + - - +
232C SER* 3.4 42.0 - - - +
233C GLN* 3.7 30.3 - - - +
236C SER* 4.0 10.1 - - - -
361C THR* 4.0 19.5 - - + +
362C VAL 4.8 0.7 - - - -
363C VAL* 4.3 21.8 - - + +
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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
----------------------------------------------------------
6C SER* 5.6 0.4 - - - -
20C CYS* 2.8 38.8 + - + +
21C TRP* 3.4 34.1 + + - +
23C LEU* 1.3 73.3 - - + +
25C CYS* 1.3 63.9 + - - +
27C GLU* 3.2 6.4 + - - +
28C HIS* 3.0 35.5 + - + -
52C PHE* 3.6 23.6 - + - -
53C PHE* 4.1 15.5 - + + -
138C PHE* 5.1 3.2 - + - -
232C SER 5.4 0.4 - - - -
235C VAL* 3.3 21.7 - - + +
236C SER* 4.1 14.6 - - - -
239C THR* 3.0 23.7 + - - +
243C ARG* 3.4 36.1 - - - -
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Residues in contact with CYS 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP 2.9 25.0 + - - +
22C GLU 3.5 5.6 - - - +
24C TYR* 1.3 76.6 - - - +
26C LEU* 1.3 61.7 + - + +
29C GLY 3.1 4.2 + - - -
30C ILE* 2.8 65.9 + - - +
53C PHE* 4.2 11.0 - - - -
83C TYR* 4.3 15.9 - - + +
86C LEU* 3.7 30.5 - - - -
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Residues in contact with LEU 26 (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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22C GLU* 3.2 18.9 + - + +
23C LEU* 3.3 8.0 + - + +
25C CYS* 1.3 77.1 - - - +
27C GLU* 1.3 63.5 + - - +
28C HIS 3.4 0.3 + - - -
29C GLY* 3.5 9.6 + - - +
30C ILE 5.0 3.6 - - - +
83C TYR* 4.6 11.0 - - - +
361C THR* 4.1 17.7 + - + +
362C VAL 3.9 6.7 - - - +
363C VAL* 3.9 20.4 - - + -
364C PRO* 3.7 31.9 - - + -
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Residues in contact with GLU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.0 32.8 + - - +
24C TYR* 3.2 7.2 + - - +
26C LEU* 1.3 78.2 - - - +
28C HIS* 1.3 58.8 + - + +
29C GLY 3.8 0.2 + - - -
233C GLN* 5.2 1.4 - - - +
236C SER* 2.5 26.5 + - - -
243C ARG* 2.7 28.1 + - - +
244C PHE* 3.5 13.5 - - + -
320C ARG* 2.9 28.9 + - - +
358C GLN* 2.8 28.8 + - + +
359C PRO 5.6 0.4 - - - +
361C THR* 3.6 27.7 + - - +
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Residues in contact with HIS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR* 3.0 25.1 + - + +
27C GLU* 1.3 74.5 - - - +
29C GLY* 1.3 62.7 + - - +
30C ILE* 3.3 16.8 + - + -
36C MET* 3.3 28.0 - - + +
38C SER* 4.4 3.1 + - - -
49C PHE* 3.7 20.9 - - + +
53C PHE* 3.8 22.4 - + - -
243C ARG* 3.4 51.3 + - + +
244C PHE* 3.4 33.9 - + - -
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Residues in contact with GLY 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C CYS 3.1 5.6 + - - -
26C LEU* 3.5 6.8 + - - -
27C GLU 3.5 3.4 + - - -
28C HIS* 1.3 78.1 - - - +
30C ILE* 1.3 60.9 + - - +
31C GLN* 3.8 4.2 + - - +
35C GLN 4.1 0.5 - - - +
36C MET* 4.0 15.1 - - - +
37C PRO* 4.2 7.4 - - - +
38C SER* 5.4 2.3 + - - -
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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) + - + + + + + -
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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