Contacts of the helix formed by residues 8 - 25 (chain C) in PDB entry 2NS7
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 LYS 8 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B GLN* 4.3 28.7 + - - +
183B GLU* 5.9 1.3 - - - +
184B PRO* 5.6 4.4 - - - +
7C SER* 1.3 71.7 - - - +
9C VAL* 1.3 57.6 + - + +
10C ILE 3.5 1.8 - - - -
11C ASN* 3.7 15.1 + - + +
12C SER* 3.1 31.3 + - - -
34C LEU* 4.1 17.0 - - + -
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Residues in contact with VAL 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER* 3.3 22.0 + - - +
8C LYS* 1.3 75.4 - - - +
10C ILE* 1.3 67.9 + - + +
12C SER* 3.4 2.1 + - - -
13C ALA* 2.9 27.7 + - - +
30C LEU* 4.2 10.9 - - + +
34C LEU* 3.8 26.7 - - + -
41C LEU* 4.1 18.2 - - + -
44C HIS* 4.0 32.3 - - + +
45C VAL* 4.7 8.7 - - + -
51C LEU* 4.8 6.7 - - + -
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Residues in contact with ILE 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER* 4.8 5.6 + - - +
8C LYS 3.5 0.4 - - - -
9C VAL* 1.3 81.0 - - + +
11C ASN* 1.3 61.9 + - - +
13C ALA* 3.0 7.1 + - - +
14C LEU* 2.8 55.1 + - + +
51C LEU* 5.2 1.6 - - + -
54C ALA* 3.9 31.6 - - + +
55C LEU* 4.0 10.8 - - + -
58C GLU* 3.7 27.4 - - + +
62C ARG* 4.7 0.2 - - - +
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Residues in contact with ASN 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 2.9 34.6 + - - -
7C SER 5.5 1.8 + - - -
8C LYS* 3.7 17.7 + - + +
9C VAL 3.5 0.2 - - - -
10C ILE* 1.3 82.7 - - - +
12C SER* 1.3 56.3 + - - +
14C LEU* 3.6 8.3 + - - +
15C GLU* 3.0 31.1 + - - +
62C ARG* 3.1 26.9 + - - -
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Residues in contact with SER 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LYS* 3.1 22.0 + - - -
9C VAL 3.6 4.7 - - - -
11C ASN* 1.3 78.0 - - - +
13C ALA* 1.3 57.0 + - - +
15C GLU* 3.4 3.2 - - - +
16C LEU* 3.0 23.9 + - - +
30C LEU* 3.7 6.8 - - - +
33C LYS* 3.3 36.5 + - - +
34C LEU* 3.5 23.7 - - - +
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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
----------------------------------------------------------
9C VAL 2.9 18.3 + - - +
10C ILE 3.5 3.1 - - - +
12C SER* 1.3 72.6 - - - +
14C LEU* 1.3 57.4 + - - +
16C LEU* 3.5 4.6 - - - +
17C LEU* 2.6 37.6 + - - +
25C LEU* 3.9 4.0 - - + +
30C LEU* 3.9 15.7 - - + +
51C LEU* 3.8 30.3 - - + -
55C LEU* 3.9 13.9 - - + -
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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
----------------------------------------------------------
10C ILE* 2.8 35.0 + - + +
11C ASN* 3.6 8.3 - - - +
13C ALA* 1.3 73.1 - - - +
15C GLU* 1.3 61.0 + - - +
17C LEU* 3.5 5.8 - - - +
18C ASN* 3.1 30.0 + - - -
55C LEU* 3.7 34.8 - - + +
58C GLU* 4.1 4.5 - - + -
59C MET* 4.4 11.2 - - + -
62C ARG* 3.5 38.1 - - - +
93C HIS* 3.5 29.1 - - + +
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Residues in contact with GLU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASN 3.0 14.5 + - - +
12C SER* 3.4 11.3 - - - +
14C LEU* 1.3 71.0 - - - +
16C LEU* 1.3 61.5 + - - +
18C ASN* 3.2 7.8 + - - +
19C GLU* 2.8 40.8 + - + +
33C LYS* 3.0 29.6 + - - +
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Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C SER 3.0 17.8 + - - +
13C ALA* 3.5 4.7 - - - +
15C GLU* 1.3 74.4 - - - +
17C LEU* 1.3 59.3 + - - +
19C GLU* 2.9 16.8 + - - +
20C VAL* 2.8 58.0 + - + +
25C LEU* 3.6 23.6 - - + -
26C THR 4.2 2.0 - - - +
29C LYS* 3.9 20.0 - - + +
30C LEU* 3.6 38.4 - - + +
33C LYS* 4.2 11.0 - - + +
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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
----------------------------------------------------------
13C ALA 2.6 20.8 + - - +
14C LEU* 3.5 7.4 - - + +
16C LEU* 1.3 73.5 - - - +
18C ASN* 1.3 58.8 + - - +
21C GLY* 2.8 32.8 + - - +
22C ILE* 3.6 29.2 - - + +
25C LEU* 4.0 16.2 - - + +
55C LEU* 4.7 9.0 - - + -
59C MET* 3.4 32.5 - - + -
93C HIS* 3.9 11.0 - - + -
94C ARG* 3.3 28.2 - - - +
99C VAL* 4.0 16.4 - - + -
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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 LEU 3.1 11.7 + - - +
15C GLU* 3.6 9.4 - - - +
17C LEU* 1.3 79.5 - - - +
19C GLU* 1.3 60.1 + - + +
92C SER 5.1 1.8 + - - -
93C HIS* 3.5 27.2 - - - +
94C ARG* 2.9 55.1 + - - +
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLU* 2.8 24.8 + - + +
16C LEU* 2.9 15.9 + - - +
18C ASN* 1.3 79.1 - - + +
20C VAL* 1.3 68.8 + - + +
33C LYS* 3.1 29.3 + - - -
94C ARG* 2.9 15.9 + - - -
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Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 2.8 42.5 + - + +
19C GLU* 1.3 80.1 - - + +
21C GLY* 1.3 63.3 + - - +
24C GLY* 3.4 42.1 + - - +
25C LEU* 3.5 4.0 - - - +
29C LYS* 4.5 13.7 - - + +
94C ARG* 3.5 12.4 + - - +
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Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 2.8 24.7 + - - -
20C VAL* 1.3 81.4 - - - +
22C ILE* 1.3 60.6 + - - -
23C GLU 3.3 2.2 - - - -
24C GLY 3.2 0.3 + - - -
25C LEU* 3.0 25.7 + - - +
94C ARG* 3.4 15.7 - - - +
95C ASP* 3.4 11.9 - - - -
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 3.6 9.3 - - + +
21C GLY* 1.3 71.6 - - - -
23C GLU* 1.3 74.8 + - + +
25C LEU* 3.4 7.8 + - - +
48C LYS* 2.6 34.0 + - - -
52C LEU* 3.6 34.1 - - + -
95C ASP* 2.9 33.9 + - + +
98C LYS* 3.9 21.1 - - + +
99C VAL* 3.4 41.5 - - + +
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Residues in contact with GLU 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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20C VAL 5.7 0.2 - - - +
21C GLY 3.3 0.8 - - - -
22C ILE* 1.3 92.9 - - + +
24C GLY* 1.3 60.2 + - - +
25C LEU 4.2 0.5 - - - +
26C THR* 4.7 5.5 - - - +
48C LYS* 3.8 10.5 + - - +
95C ASP* 4.6 0.9 + - - +
98C LYS* 5.0 11.1 - - - +
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Residues in contact with GLY 24 (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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20C VAL* 3.4 20.7 + - - +
21C GLY 3.2 5.8 + - - -
23C GLU* 1.3 76.1 - - - +
25C LEU* 1.3 64.2 + - - +
26C THR* 3.1 8.0 + - - +
29C LYS* 3.2 38.5 + - - +
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ALA* 3.9 13.7 - - + +
16C LEU* 3.6 36.8 - - + -
17C LEU* 4.0 13.9 - - + +
20C VAL* 3.5 4.9 - - + +
21C GLY 3.0 13.0 + - - +
22C ILE* 3.5 11.0 - - + +
23C GLU 3.4 0.4 - - - -
24C GLY* 1.3 74.7 - - - +
26C THR* 1.3 60.3 + - - +
30C LEU* 5.1 0.7 - - + -
48C LYS* 2.5 36.1 + - + +
51C LEU* 4.0 22.0 - - + -
52C LEU* 3.8 29.2 - - + -
55C LEU* 3.9 18.4 - - + -
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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