Contacts of the helix formed by residues 4 - 21 (chain B) in PDB entry 1NSH
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 4 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU* 3.9 17.7 + - - +
43A LEU* 5.7 0.4 - - + -
1B SER* 3.5 24.0 - - - +
2B ARG 3.1 1.7 - - - +
3B PRO* 1.3 81.6 - - - +
5B GLU* 1.3 59.8 + - - +
6B THR* 3.3 14.6 + - - -
7B GLU* 2.6 64.9 + - + +
8B ARG* 3.1 7.2 + - - +
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Residues in contact with GLU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 3.8 6.1 + - - +
19A LYS* 6.1 4.3 - - - +
42A GLU* 5.8 2.5 - - - +
3B PRO 3.5 3.7 + - - +
4B THR* 1.3 74.1 + - - +
6B THR* 1.3 63.8 + - - +
8B ARG* 2.9 36.5 + - - +
9B CYS* 3.1 20.1 + - - +
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Residues in contact with THR 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.8 5.0 - - + +
38A PHE* 3.6 24.9 - - + -
42A GLU* 3.1 38.9 + - - +
43A LEU* 3.5 28.7 - - + -
80A ILE* 5.1 0.9 - - + -
4B THR* 3.0 2.1 + - - -
5B GLU* 1.3 75.5 - - - +
7B GLU* 1.3 55.9 + - - +
9B CYS* 2.8 37.7 + - - -
10B ILE* 2.6 23.0 - - + +
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 5.0 2.0 - - + +
45A ALA* 4.5 5.7 - - - +
46A PHE* 4.0 16.1 - - - -
88A HIS* 3.5 26.2 + - - -
1B SER* 3.1 23.0 - - - +
2B ARG* 2.8 40.6 - - - +
4B THR* 2.6 39.2 + - + +
6B THR* 1.3 74.6 - - - +
8B ARG* 1.3 59.1 + - - -
10B ILE* 3.4 6.8 + - + +
11B GLU* 3.4 20.3 + - - +
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Residues in contact with ARG 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 4.2 2.7 - - - +
2B ARG 4.5 9.2 - - - +
3B PRO* 4.3 18.0 + - + +
4B THR 3.1 6.3 + - - +
5B GLU* 2.9 32.7 + - - +
7B GLU* 1.3 80.1 - - - +
9B CYS* 1.3 62.6 + - - +
11B GLU* 4.1 5.1 - - - +
12B SER* 3.1 24.6 + - - -
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Residues in contact with CYS 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 2.8 37.9 + - - +
13A LEU* 2.7 38.1 - - - +
16A VAL* 3.5 22.7 - - + -
80A ILE* 4.7 0.2 - - - -
5B GLU 3.1 12.8 + - - +
6B THR* 2.8 30.3 + - - +
8B ARG* 1.3 75.5 - - - +
10B ILE* 1.3 72.6 + - - +
12B SER* 3.2 14.7 - - - -
13B LEU 3.6 0.9 + - - -
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Residues in contact with ILE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.0 4.0 - - - -
43A LEU* 3.3 25.6 - - + -
46A PHE* 3.8 21.1 - - + -
80A ILE* 3.0 29.4 - - + -
84A ALA* 3.2 35.7 - - + -
88A HIS* 4.2 3.1 - - + -
6B THR* 2.6 42.5 + - + +
7B GLU* 3.6 10.5 - - - +
9B CYS* 1.3 75.9 - - - +
11B GLU* 1.3 63.7 + - - +
12B SER 2.9 1.6 + - - -
13B LEU* 3.2 10.0 + - - +
14B ILE* 2.8 26.4 + - + +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A HIS* 3.5 15.9 - - + -
89A GLU* 2.7 37.3 - - - +
7B GLU 3.4 13.7 + - - +
8B ARG* 4.2 5.6 - - - +
10B ILE* 1.3 78.7 - - - +
12B SER* 1.3 61.3 + - - +
14B ILE* 3.4 9.7 - - - +
15B ALA* 3.3 32.6 + - - +
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Residues in contact with SER 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 3.8 5.9 + - - +
8A ARG* 4.2 2.4 - - - +
9A CYS* 2.8 40.1 + - - +
12A SER* 4.8 0.6 - - - -
8B ARG 3.1 16.1 + - - -
9B CYS* 3.2 14.4 - - - -
10B ILE 2.9 1.4 + - - -
11B GLU* 1.3 81.1 - - - +
13B LEU* 1.3 60.1 + - - -
15B ALA* 4.0 2.3 - - - +
16B VAL* 3.0 25.1 + - - +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A CYS* 2.7 54.1 - - - +
10A ILE* 3.7 2.5 - - - +
13A LEU* 4.0 18.8 - - + -
77A LEU* 4.9 2.0 - - + -
9B CYS 3.6 1.7 + - - +
10B ILE 3.2 6.4 + - - +
12B SER* 1.3 77.7 - - - +
14B ILE* 1.3 62.0 + - + +
16B VAL* 2.6 28.0 - - + +
17B PHE* 3.7 3.8 + - - +
76B PHE* 4.9 0.7 - - - +
77B LEU* 3.3 34.8 - - + +
80B ILE* 3.1 40.6 - - + -
81B GLY* 5.1 0.7 - - - +
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Residues in contact with ILE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA* 3.8 14.6 - - + -
88A HIS* 3.6 24.5 - - + +
89A GLU* 4.0 16.2 - - + +
90A SER* 3.7 31.2 - - - +
10B ILE* 2.8 44.1 + - + +
11B GLU* 3.4 10.1 - - - +
13B LEU* 1.3 77.6 - - + +
15B ALA* 1.3 53.7 + - - +
17B PHE* 3.5 7.5 + - - +
18B GLN* 2.7 41.9 + - + +
77B LEU* 5.6 7.6 - - + -
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU* 5.2 4.3 - - - +
11B GLU* 3.3 27.2 + - - +
12B SER* 4.0 3.4 - - - +
13B LEU 3.2 0.2 - - - -
14B ILE* 1.3 77.3 - - + +
16B VAL* 1.3 59.4 + - - +
17B PHE 2.9 2.0 - - - -
18B GLN* 3.8 11.0 - - + -
19B LYS* 2.6 44.0 + - - +
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU 5.9 0.2 - - - -
6A THR* 3.8 7.0 - - + +
9A CYS* 3.5 25.4 - - + -
12B SER 3.0 17.0 - - - +
13B LEU* 2.6 35.7 - - + +
15B ALA* 1.3 77.5 - - - +
17B PHE* 1.3 69.2 + - - +
19B LYS* 4.0 1.9 - - - +
20B TYR* 3.9 7.8 + - - +
38B PHE* 3.3 40.8 - - + -
76B PHE* 3.3 34.8 - - + -
80B ILE* 4.9 0.4 - - + -
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Residues in contact with PHE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A SER* 3.1 20.9 - - - -
13B LEU 4.2 4.5 - - - +
14B ILE* 3.5 9.9 - - + +
15B ALA 2.9 0.4 - - - -
16B VAL* 1.3 79.4 - - - +
18B GLN* 1.3 85.2 + - - +
20B TYR* 3.1 5.7 + - - +
21B ALA* 2.6 57.8 + - + +
28B VAL 3.3 26.2 - - - -
29B THR 3.5 11.2 - - - -
30B LEU* 3.7 6.0 - - + +
71B LEU* 5.5 0.2 - - + -
72B ASP 2.7 29.8 - - - -
73B PHE* 4.1 7.4 - - - +
76B PHE* 3.4 38.4 - + + -
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Residues in contact with GLN 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU* 3.5 12.9 - - + +
90A SER* 2.6 39.6 + - - +
14B ILE* 2.7 30.8 + - + +
15B ALA* 3.8 8.7 - - + +
17B PHE* 1.3 107.9 - - - +
19B LYS* 1.3 53.3 + - - +
21B ALA* 3.8 5.8 + - - +
22B GLY 2.5 45.9 + - - +
27B SER 5.1 5.7 + - - -
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 6.1 4.2 - - - +
15B ALA* 2.6 29.5 + - - +
16B VAL* 4.0 6.9 - - - +
18B GLN* 1.3 74.3 - - - +
20B TYR* 1.3 67.3 + - + +
22B GLY 3.7 4.6 + - - -
23B LYS* 3.2 42.8 - - + +
38B PHE* 5.0 7.1 - - + -
42B GLU* 4.5 15.1 + - - +
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Residues in contact with TYR 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL 3.9 3.9 + - - +
17B PHE 3.1 2.9 + - - +
19B LYS* 1.3 81.0 - - + +
21B ALA* 1.3 57.8 + - - +
22B GLY 3.1 9.0 + - - -
23B LYS* 4.8 13.9 + - - +
30B LEU* 3.2 30.7 - - + +
34B GLU* 2.7 55.4 - - + +
37B SER* 2.6 34.2 + - - -
38B PHE* 3.3 45.3 + + + -
41B THR* 4.0 9.5 - - + +
42B GLU* 5.3 1.3 - - + -
76B PHE* 4.9 0.7 - - + -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 2.6 50.4 + - + +
18B GLN* 3.1 7.2 + - - +
20B TYR* 1.3 73.3 - - - +
22B GLY* 1.3 53.7 + - - +
26B HIS* 4.9 1.4 - - - +
27B SER* 3.8 19.3 + - - +
29B THR 2.8 31.7 - - - +
30B LEU* 3.4 8.5 - - + +
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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