Contacts of the helix formed by residues 10 - 23 (chain C) in PDB entry 2XN9
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 THR 10 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C GLU 3.9 2.9 + - - +
9C LEU* 1.3 76.2 - - - +
11C ASP* 1.3 64.8 + - - +
12C LEU* 3.6 3.2 + - - -
13C ALA* 2.8 30.1 + - - +
14C LEU* 3.1 11.7 + - - +
184C GLU* 2.9 37.7 + - + +
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Residues in contact with ASP 11 (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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28A VAL* 4.4 15.4 - - + +
9C LEU 4.7 3.1 - - - +
10C THR* 1.3 71.2 - - - +
12C LEU* 1.3 63.4 + - - +
14C LEU* 3.3 12.6 + - - +
15C ALA* 3.0 24.8 + - - +
155C LYS* 3.1 42.9 + - - +
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Residues in contact with LEU 12 (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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28A VAL* 4.1 12.9 - - + +
67A ASP 4.8 0.4 - - - +
68A ALA* 3.6 46.7 - - + +
69A ARG* 4.0 14.6 - - + -
10C THR* 3.1 2.1 + - - +
11C ASP* 1.3 80.0 - - - +
13C ALA* 1.3 51.8 + - - +
15C ALA* 3.3 2.0 + - - -
16C ASN* 2.8 51.3 + - - +
184C GLU* 3.5 36.3 - - + +
185C ASN* 4.1 15.3 - - - +
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Residues in contact with ALA 13 (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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9C LEU* 4.2 14.1 - - + -
10C THR* 2.8 35.8 + - - +
12C LEU* 1.3 72.5 - - - +
14C LEU* 1.3 55.4 + - - +
16C ASN* 3.5 1.7 + - - +
17C ALA* 2.9 29.1 + - - +
181C LEU* 3.7 15.8 - - + +
183C GLY 4.6 1.8 - - - +
184C GLU* 3.6 26.9 - - + +
189C ILE* 4.0 1.4 - - - +
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Residues in contact with LEU 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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6C LYS* 3.8 23.6 - - + +
9C LEU* 3.7 38.6 - - + +
10C THR 3.1 14.2 + - - +
11C ASP* 3.6 12.3 - - - +
13C ALA* 1.3 73.6 - - - +
15C ALA* 1.3 61.3 + - - +
17C ALA* 3.3 4.3 + - - +
18C TYR* 2.8 30.8 + - - +
153C TYR* 3.6 41.1 - - + +
155C LYS* 3.9 33.4 - - + +
181C LEU* 5.4 0.2 - - + -
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Residues in contact with ALA 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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28A VAL* 3.4 33.4 - - + -
29A PHE 4.7 2.2 - - - +
30A SER* 5.0 9.8 - - - +
69A ARG* 3.7 20.1 + - - -
11C ASP 3.0 11.4 + - - +
12C LEU 3.7 2.2 - - - +
14C LEU* 1.3 75.1 - - - +
16C ASN* 1.3 58.6 + - - +
18C TYR* 3.4 8.5 + - - +
19C GLY* 2.9 24.3 + - - -
153C TYR 5.5 0.2 - - - -
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Residues in contact with ASN 16 (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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52A GLY* 4.9 2.8 + - - -
67A ASP 5.1 5.2 + - - +
69A ARG* 2.8 34.8 + - - +
12C LEU* 2.8 35.9 + - - +
13C ALA 3.9 2.0 - - - +
15C ALA* 1.3 73.7 - - - +
17C ALA* 1.3 56.7 + - - +
19C GLY* 3.3 0.9 + - - -
20C GLN* 2.9 34.0 + - - +
184C GLU 3.0 25.8 + - - +
185C ASN* 3.6 16.0 + - - +
186C ASP* 3.2 24.3 + - - +
189C ILE* 3.9 7.6 - - + -
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Residues in contact with ALA 17 (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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13C ALA 2.9 18.6 + - - +
14C LEU 3.3 3.3 + - - +
16C ASN* 1.3 71.7 - - - +
18C TYR* 1.3 66.7 + - - +
20C GLN* 3.3 2.8 + - - -
21C TYR* 3.0 36.9 + - + +
153C TYR* 3.9 27.6 - - + -
181C LEU* 3.9 21.8 - - + -
189C ILE* 3.9 8.6 - - + +
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Residues in contact with TYR 18 (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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30A SER* 4.7 11.7 - - - -
94A SER* 3.7 47.8 + - - -
101B TYR* 5.0 11.7 + - - -
14C LEU 2.8 21.7 + - - +
15C ALA* 3.5 7.9 - - - +
17C ALA* 1.3 71.5 - - - +
19C GLY* 1.3 61.6 + - - +
22C ASN* 2.7 63.5 + - + +
23C HIS* 5.0 2.9 - + - -
147C SER* 3.3 26.5 - - - -
148C ASP* 5.3 1.6 + - - -
153C TYR* 4.0 24.2 - - + +
154C TYR 5.4 0.4 - - - -
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Residues in contact with GLY 19 (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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50A VAL 4.5 4.0 - - - -
51A THR* 5.0 2.8 + - - -
69A ARG* 3.8 15.7 - - - -
15C ALA 2.9 15.0 + - - -
16C ASN 3.7 3.4 - - - -
17C ALA 3.2 0.2 - - - -
18C TYR* 1.3 79.7 - - - +
20C GLN* 1.3 69.4 + - - +
23C HIS* 3.2 34.8 + - - +
1216C NA 4.2 2.9 - - - -
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Residues in contact with GLN 20 (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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51A THR* 3.9 8.0 - - - +
69A ARG* 5.5 0.3 + - - -
16C ASN 2.9 21.2 + - - +
17C ALA* 3.9 6.1 - - - +
19C GLY* 1.3 80.0 - - - +
21C TYR* 1.3 69.2 + - + +
22C ASN 3.5 0.3 + - - -
23C HIS 3.7 7.5 + - - -
24C PRO* 3.9 11.6 - - - +
76C ALA* 3.4 24.4 - - + +
77C SER 3.1 30.0 + - - +
78C PHE 4.2 0.2 - - - +
140C ILE* 5.1 0.3 - - - +
186C ASP* 3.0 37.4 - - + +
189C ILE* 5.0 3.6 - - + -
190C ASP* 2.7 40.1 + - - +
1216C NA 4.1 1.3 - - - -
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Residues in contact with TYR 21 (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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17C ALA* 3.0 32.8 + - + +
18C TYR 4.5 0.9 - - - +
20C GLN* 1.3 82.1 - - + +
22C ASN* 1.3 63.8 + - - +
23C HIS 3.6 0.2 - - - -
24C PRO* 4.4 3.3 - - - +
76C ALA* 5.3 2.9 - - + -
139C ASP* 4.5 0.2 - - - -
140C ILE* 3.8 44.7 - - + +
143C ARG* 3.3 55.8 + - + +
144C LYS* 3.9 21.1 - - - +
147C SER* 5.9 0.4 - - - -
153C TYR* 3.8 21.5 - + + -
181C LEU* 5.3 0.7 - - + -
189C ILE* 4.6 16.5 - - + +
190C ASP* 5.2 2.7 - - - -
192C ILE* 4.2 4.5 - - - +
193C TYR* 2.5 39.9 + + - -
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Residues in contact with ASN 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 TYR* 2.7 59.0 + - + +
21C TYR* 1.3 81.9 - - - +
23C HIS* 1.3 82.2 + - + +
24C PRO* 3.5 8.0 - - - +
144C LYS* 3.3 35.6 - - + +
147C SER* 3.3 26.7 + - - -
148C ASP* 3.9 4.5 - - - +
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Residues in contact with HIS 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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50A VAL* 3.8 34.9 + - + +
51A THR* 5.1 1.6 - - - +
101B TYR* 2.7 41.0 + + - -
18C TYR* 5.0 6.3 - + - -
19C GLY* 3.2 20.3 + - - +
20C GLN 3.7 2.4 + - - -
21C TYR 3.6 0.2 - - - -
22C ASN* 1.3 102.1 + - + +
24C PRO* 1.3 64.6 - - - +
77C SER* 3.4 1.2 + - - -
1216C NA 2.2 34.6 - - - -
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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