Contacts of the helix formed by residues 25 - 38 (chain C) in PDB entry 6A5T
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 25 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL* 1.3 86.3 - - - +
26C LEU* 1.3 63.2 + - - +
27C SER* 4.1 1.8 + - - +
28C LEU* 4.1 22.7 - - + +
29C ALA 4.0 5.9 + - - -
225C PRO 4.8 4.5 - - - -
228C PHE* 2.8 15.9 - - - -
45K LEU* 6.1 0.8 - - - +
48K GLU* 3.0 38.6 + - - +
49K GLU* 4.9 6.1 + - - +
52K LEU* 4.2 15.8 - - - +
97K LYS* 4.7 14.6 + - - +
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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
----------------------------------------------------------
1077B THR 3.2 24.9 - - - +
1078B GLY* 4.6 4.3 - - - -
1079B LYS* 3.3 28.0 - - + +
25C ASN* 1.3 72.9 - - - +
27C SER* 1.3 68.2 + - - +
28C LEU 3.0 2.5 + - - -
29C ALA* 3.2 2.9 + - - +
30C ASN* 3.0 18.1 + - + +
178C PHE* 4.7 7.4 - - + -
180C TYR* 3.6 26.9 - - + +
188C HIS* 5.8 1.3 - - + -
225C PRO* 4.2 19.6 + - + +
228C PHE* 3.3 26.2 - - + -
48K GLU* 4.2 3.0 + - - -
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Residues in contact with SER 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077B THR* 4.9 2.4 + - - -
25C ASN* 4.3 0.3 + - - +
26C LEU* 1.3 80.1 - - - +
28C LEU* 1.3 58.1 + - - +
30C ASN* 3.7 7.7 - - - +
31C SER* 2.8 32.4 + - - -
44K ASN* 3.7 31.7 + - - +
45K LEU* 3.5 13.4 + - - +
47K ARG* 5.8 0.2 - - - -
48K GLU* 2.2 41.8 + - - +
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 5.2 2.9 - - + -
24C VAL* 4.6 21.3 - - + -
25C ASN* 4.1 29.5 - - + +
26C LEU 3.0 1.0 - - - -
27C SER* 1.3 79.4 + - - +
29C ALA* 1.3 66.4 + - - +
31C SER* 3.8 2.0 - - - -
32C LEU* 3.0 26.0 + - + +
251C LEU* 6.1 2.2 - - + -
45K LEU* 3.5 20.6 - - + -
48K GLU* 4.1 0.6 + - - -
94K ILE* 5.3 6.7 - - + -
97K LYS* 4.8 20.9 - - + -
98K LEU* 4.1 30.5 - - + -
101K LEU* 4.9 9.6 - - + -
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 4.9 7.0 - - + -
24C VAL* 5.2 1.4 - - + +
25C ASN 4.0 2.0 + - - -
26C LEU 3.2 8.0 + - - +
28C LEU* 1.3 80.2 - - - +
30C ASN* 1.3 58.4 + - - +
32C LEU* 3.3 8.3 + - - +
33C ARG* 2.9 26.9 + - - +
178C PHE* 3.8 28.7 - - + -
228C PHE* 4.0 26.7 - - + -
230C MET* 4.3 11.1 - - + +
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Residues in contact with ASN 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001B PHE* 5.4 0.2 - - - -
1075B GLY 3.4 6.6 + - - +
1076B HIS 3.2 8.7 + - - -
1077B THR* 3.0 23.9 - - - +
1078B GLY* 2.8 33.9 - - - +
26C LEU* 3.0 13.9 + - + +
27C SER* 3.7 8.7 - - - +
29C ALA* 1.3 74.8 - - - +
31C SER* 1.3 65.7 + - - +
33C ARG* 3.0 31.8 + - - +
34C ARG* 3.0 27.6 + - - +
178C PHE* 4.9 5.1 - - + -
44K ASN* 4.1 3.0 - - - +
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Residues in contact with SER 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C SER 2.8 16.0 + - - -
28C LEU* 3.8 3.8 - - - -
30C ASN* 1.3 72.7 - - - +
32C LEU* 1.3 63.1 + - - +
34C ARG* 3.3 4.9 + - - +
35C THR* 2.9 27.6 + - - -
251C LEU* 4.3 7.6 - - - -
40K HIS 4.8 0.7 + - - -
41K THR* 3.3 32.7 + - - +
44K ASN* 5.0 2.6 - - - +
45K LEU* 3.1 39.4 + - - +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 4.9 9.6 - - + -
28C LEU* 3.0 20.5 + - + +
29C ALA* 3.5 8.5 - - - +
30C ASN 3.1 0.2 - - - -
31C SER* 1.3 76.8 - - - +
33C ARG* 1.3 64.6 + - - +
35C THR* 3.2 5.3 + - - -
36C MET* 2.9 44.3 + - + +
230C MET* 4.1 18.2 - - + -
244C PHE* 3.4 37.7 - - + -
247C GLY* 4.8 12.1 - - - -
248C ILE* 4.6 13.7 - - + -
251C LEU* 4.9 8.9 - - + +
98K LEU* 6.0 3.4 - - + -
101K LEU* 5.7 3.8 - - + -
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Residues in contact with ARG 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B GLU* 4.2 17.8 + - - +
1001B PHE* 2.9 55.8 - - - +
1075B GLY* 3.4 23.4 + - - -
29C ALA 2.9 13.3 + - - +
30C ASN* 3.0 28.1 + - - +
32C LEU* 1.3 77.2 - - - +
34C ARG* 1.3 70.9 + - - +
35C THR 3.2 0.2 + - - -
36C MET* 3.2 12.1 + - + +
37C LEU* 3.0 28.0 + - + +
176C ILE* 3.5 40.6 + - + +
178C PHE* 4.4 12.6 - - + -
230C MET* 5.8 0.9 - - + -
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Residues in contact with ARG 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995B ARG* 4.7 0.2 - - - +
997B GLU* 3.4 34.2 + - + +
998B ASP* 2.3 32.6 + - - -
1075B GLY 3.8 23.1 + - - +
1076B HIS* 4.1 3.8 + - - -
30C ASN* 3.0 24.1 + - - +
31C SER 3.9 2.9 - - - +
33C ARG* 1.3 82.0 - - - +
35C THR* 1.3 57.6 + - - +
37C LEU* 3.3 0.9 + - - +
38C ALA* 2.9 33.0 + - + +
39K ASP* 3.1 15.0 + - - +
40K HIS* 3.1 30.1 - - - +
41K THR* 2.3 61.4 + - - +
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Residues in contact with THR 35 (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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31C SER 2.9 19.1 + - - -
32C LEU* 3.6 7.6 - - - -
33C ARG 3.1 0.4 - - - -
34C ARG* 1.3 75.4 - - - +
36C MET* 1.3 67.2 + - - +
37C LEU 3.0 1.2 + - - -
38C ALA 3.8 0.2 - - - -
39C GLU* 3.2 33.2 + - + +
40C VAL* 3.7 9.6 - - + +
247C GLY* 3.5 37.0 - - - +
250C THR* 4.6 9.9 - - + -
251C LEU* 3.8 16.4 - - + +
41K THR* 3.7 15.3 - - - +
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Residues in contact with MET 36 (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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32C LEU* 2.9 55.9 + - + +
33C ARG* 3.2 14.1 + - + -
35C THR* 1.3 75.8 - - - +
37C LEU* 1.3 63.9 + - - +
40C VAL* 4.4 8.1 - - - -
172C PRO* 4.1 6.6 - - - +
173C CYS* 3.5 23.0 - - - +
176C ILE* 3.6 17.9 - - + -
230C MET* 4.0 15.7 - - - +
232C VAL* 3.5 28.7 - - + -
243C VAL* 4.0 25.6 - - + +
244C PHE* 4.6 9.9 - - - -
247C GLY* 5.0 4.7 - - - -
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Residues in contact with LEU 37 (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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996B HIS* 3.8 34.2 - - + +
997B GLU* 4.9 17.5 - - + +
33C ARG* 3.0 20.5 + - - +
34C ARG* 4.2 3.8 - - - +
35C THR 3.0 1.2 - - - -
36C MET* 1.3 88.5 - - - +
38C ALA* 1.3 61.4 + - - +
164C ALA* 3.6 11.8 - - - +
171C SER* 4.6 7.0 + - - +
172C PRO* 4.3 8.9 - - - +
173C CYS* 3.4 30.1 - - + +
174C SER 3.9 9.0 - - - +
176C ILE* 3.7 33.2 - - + +
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Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995B ARG* 4.4 20.2 - - - +
997B GLU* 4.7 7.4 - - - +
34C ARG* 2.9 17.2 + - + +
37C LEU* 1.3 78.3 - - - +
39C GLU* 1.3 73.5 + - + +
40C VAL 3.2 7.5 + - - -
163C ILE 4.1 0.2 - - - -
164C ALA* 2.9 37.5 + - + +
165C LYS* 5.1 5.2 - - + +
170C TRP 4.4 3.1 - - - +
172C PRO* 4.6 0.9 - - - +
41K THR* 6.0 1.1 - - - +
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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
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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