Contacts of the strand formed by residues 9 - 23 (chain A) in PDB entry 5NXR
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 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.7 31.5 - - + -
5A ASN* 3.4 21.5 + - - -
6A LYS 3.3 13.1 + - - +
7A ASP 4.8 1.3 - - - +
8A GLY* 1.3 80.5 - - - +
10A LYS* 1.3 62.7 + - - +
11A LEU* 4.3 4.1 - - - +
47A ASP 3.2 7.2 - - - +
1C ALA* 5.7 1.0 - - - +
315C ASN* 3.2 32.3 + - - +
350C TYR* 2.7 28.9 + - - -
352C PHE* 4.4 15.6 + - - +
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Residues in contact with LYS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GLU* 3.5 30.8 + - - +
4A TYR 3.3 6.7 - - - +
5A ASN* 4.2 14.6 - - - +
9A ASN* 1.3 74.2 - - - +
11A LEU* 1.3 63.9 + - - +
12A ASP* 4.3 4.0 - - - -
45A LYS 4.0 0.3 - - - +
46A GLY* 3.3 4.5 - - - -
47A ASP* 2.8 70.8 + - + +
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GLU* 3.8 5.4 + - - -
3A VAL* 2.9 40.7 + - + +
4A TYR* 3.1 30.5 + - + -
9A ASN* 4.3 6.3 - - - +
10A LYS* 1.3 80.5 - - - +
12A ASP* 1.3 61.6 + - - +
13A VAL* 4.8 5.4 - - + -
44A VAL* 4.2 16.6 - - + -
45A LYS 3.7 0.7 - - - +
46A GLY* 3.9 15.0 - - - +
13C VAL* 6.0 1.1 - - + -
350C TYR* 4.0 4.0 - - - +
352C PHE* 3.7 54.1 - - + -
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Residues in contact with ASP 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA* 3.0 40.5 - - - +
2A GLU* 3.0 13.6 + - - +
10A LYS* 6.2 3.8 - - - -
11A LEU* 1.3 72.6 - - - +
13A VAL* 1.3 62.2 + - - +
14A TYR* 4.2 15.6 + - - +
43A GLY 4.0 0.3 - - - +
44A VAL* 3.4 6.9 - - - +
45A LYS* 2.8 64.1 + - + +
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Residues in contact with VAL 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ALA 2.5 36.5 + - - -
3A VAL* 4.1 25.5 - - + +
11A LEU* 4.2 5.6 + - + -
12A ASP* 1.3 77.0 - - - +
14A TYR* 1.3 68.4 + - - +
43A GLY 3.5 8.3 - - - +
44A VAL* 4.4 16.4 - - + -
352A PHE* 4.3 13.5 - - + +
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Residues in contact with TYR 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA* 5.0 0.7 - - - +
12A ASP* 4.2 20.0 - - - +
13A VAL* 1.3 80.8 - - - +
15A GLY* 1.3 62.0 + - - +
41A ARG* 4.7 8.5 - - - -
42A LEU* 3.6 3.8 - - - +
43A GLY* 2.8 61.3 + - - +
44A VAL 3.9 2.7 - - - -
45A LYS* 4.2 26.7 - - + -
59A ARG* 3.0 22.3 + - - -
60A PHE 4.0 1.0 + - - -
61A GLU* 2.6 42.6 + - + +
352A PHE* 3.7 22.9 - - - +
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 1.3 83.5 - - - +
16A LYS* 1.3 62.4 - - - +
41A ARG* 2.9 16.6 - - - -
42A LEU* 4.2 0.7 - - - -
351A GLN* 3.7 2.1 - - - +
352A PHE* 2.9 48.6 + - - +
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLY* 1.3 75.5 - - - +
17A VAL* 1.3 62.1 + - - +
18A ASP* 3.1 35.4 + - + -
20A ARG* 4.8 3.2 - - - +
39A ARG* 5.1 6.7 - - - +
40A VAL* 3.4 7.1 - - - +
41A ARG* 2.8 85.3 + - + +
42A LEU* 6.1 0.2 - - - -
63A GLU* 4.6 2.9 + - - -
349A VAL* 4.2 10.1 - - + -
350A TYR 3.3 11.0 - - - +
351A GLN* 4.0 19.1 - - + +
352A PHE* 4.6 2.8 - - - -
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 1.3 75.2 - - - +
18A ASP* 1.3 59.9 + - - +
19A VAL* 3.9 9.9 - - + -
39A ARG 4.1 1.6 - - - +
40A VAL* 4.3 14.8 - - + -
348A LEU 3.7 1.9 - - - +
349A VAL* 3.3 4.0 - - - +
350A TYR* 2.8 48.6 + - + +
352A PHE* 5.0 8.7 - - + -
44B VAL* 5.9 0.7 - - + -
58B GLY* 4.5 5.8 - - - -
59B ARG* 4.2 25.8 - - - +
60B PHE* 4.6 9.4 - - + +
80B ALA 4.2 3.6 - - - -
81B TYR 3.6 36.1 - - - +
82B ALA* 4.6 2.3 - - + +
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Residues in contact with ASP 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 3.1 31.1 + - + -
17A VAL* 1.3 71.0 - - - +
19A VAL* 1.3 60.6 + - - +
20A ARG* 2.8 39.8 + - - +
38A SER* 3.3 2.9 - - - -
39A ARG* 2.8 57.6 + - + +
113A LEU* 5.1 1.7 - - - +
319A VAL* 5.9 0.2 - - - +
347A GLY* 5.2 0.5 - - - -
348A LEU 3.8 3.0 + - - -
349A VAL* 3.5 25.0 - - + +
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Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.0 12.8 - - + -
18A ASP* 1.3 76.8 - - - +
20A ARG* 1.3 61.1 + - - +
38A SER* 3.2 15.3 - - - +
39A ARG 5.6 0.4 - - - +
347A GLY* 3.2 4.5 - - - -
348A LEU* 2.9 58.9 + - + +
402A LDA 3.9 1.2 - - + +
80B ALA* 3.9 18.2 - - + +
81B TYR* 4.0 7.2 - - - -
82B ALA* 4.0 9.0 - - + +
94B TYR* 3.6 44.0 - - + +
95B GLY* 4.2 0.9 - - - -
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Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 4.8 2.8 - - - +
18A ASP* 2.8 35.8 + - - +
19A VAL* 1.3 81.6 - - - +
21A HIS* 1.3 58.6 + - - +
22A TYR* 3.2 32.3 + - + -
36A ASP* 3.3 9.4 - - - +
37A ASP 3.0 44.2 + - - +
38A SER* 2.9 7.1 + - - -
39A ARG* 3.4 28.5 - - - +
112A PRO 4.9 3.8 + - - -
113A LEU* 3.5 47.7 + - + +
346A LEU 3.3 8.1 - - - +
347A GLY* 4.5 0.7 - - - -
402A LDA 4.8 0.2 - - - -
94B TYR* 3.4 8.4 + - - -
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Residues in contact with HIS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG* 1.3 73.8 - - - +
22A TYR* 1.3 88.9 + - - +
23A PHE* 3.6 36.9 - + + -
34A ASP* 4.2 5.8 + - - -
35A GLY* 3.4 12.8 - - - -
344A LEU 3.9 1.0 - - - +
345A GLY* 3.5 0.2 - - - -
346A LEU* 2.8 36.0 + - - +
402A LDA 4.0 44.9 - - + +
94B TYR* 3.2 14.9 + - + +
132B ASN* 2.9 38.0 + - - -
156B GLY* 4.5 3.6 - - - -
157B LYS 5.7 0.2 - - - -
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Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG* 3.2 44.1 + - + -
21A HIS* 1.3 88.0 - - - +
23A PHE* 1.3 59.3 + - - +
24A ALA 4.1 0.2 - - - -
33A GLU* 3.3 31.4 - - - +
34A ASP* 2.9 5.8 - - - +
35A GLY 2.7 37.5 + - - +
37A ASP* 2.8 36.1 + - + -
39A ARG* 4.1 0.2 + - - -
113A LEU* 4.3 11.0 - - + -
114A TRP* 3.7 34.0 - + - -
343A VAL* 3.8 11.0 - - + -
344A LEU 3.4 2.7 - - - -
345A GLY* 3.8 9.4 - - - -
163B LYS* 3.8 14.4 - - + -
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Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A HIS* 3.6 28.7 - + - -
22A TYR* 1.3 72.9 - - - +
24A ALA* 1.3 63.8 + - - +
34A ASP* 3.6 4.7 - - - -
343A VAL* 3.6 1.0 - - - +
344A LEU* 2.7 58.3 + - + +
346A LEU* 3.6 34.3 - - + -
402A LDA 3.7 48.0 - - + -
403A LDA 3.4 56.7 - - + -
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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