Contacts of the helix formed by residues 17 - 32 (chain A) in PDB entry 1SXP
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 17 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN 4.6 3.1 + - - -
14A ASN* 4.4 1.2 + - - -
15A PHE 3.2 0.4 - - - -
16A LYS* 1.3 89.3 - - + +
18A VAL* 1.3 66.9 + - - +
19A PRO* 4.0 6.2 - - - +
20A SER* 3.0 26.0 + - - -
21A SER* 2.9 26.3 + - - -
240A MET* 3.9 6.7 - - - -
5C C 3.6 45.9 + - - +
6C T 3.7 10.9 + - - +
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 1.3 76.2 - - - +
19A PRO* 1.3 75.1 - - + +
21A SER* 3.1 4.9 + - - -
22A GLU* 3.1 21.7 + - + +
240A MET* 4.7 11.1 - - + -
6C T 4.1 5.6 + - - +
7C A 5.2 16.6 - - + +
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Residues in contact with PRO 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 4.0 4.5 + - - +
10A ASN* 3.6 37.5 - - + +
11A ASN 5.4 0.9 - - - +
12A VAL* 5.4 0.2 - - - -
17A THR* 3.8 4.5 - - - +
18A VAL* 1.3 101.1 - - + +
20A SER* 1.3 62.8 + - - +
22A GLU* 3.5 11.9 + - + +
23A THR* 3.0 27.2 + - - -
6C T 3.7 28.9 - - - +
7C A 3.8 18.2 - - + +
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN 3.9 12.3 + - - -
12A VAL* 3.3 11.4 - - - +
13A ILE 3.0 24.9 + - - -
14A ASN* 2.7 26.3 + - - -
17A THR* 3.0 20.6 + - - -
18A VAL 3.2 1.4 + - - -
19A PRO* 1.3 81.5 - - - +
21A SER* 1.3 62.6 + - - +
23A THR* 3.3 2.8 + - - -
24A ILE* 3.0 28.1 + - - +
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Residues in contact with SER 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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14A ASN 3.8 1.1 + - - -
15A PHE* 3.1 44.6 + - - +
17A THR 2.9 21.8 + - - -
18A VAL* 3.6 4.5 - - - -
20A SER* 1.3 74.2 - - - +
22A GLU* 1.3 57.0 + - - +
24A ILE* 3.2 1.5 + - - +
25A TYR* 2.7 50.3 + - - +
240A MET* 5.1 8.5 + - - +
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 4.8 0.2 + - - -
18A VAL* 3.1 15.2 + - + +
19A PRO* 3.6 10.7 - - + +
20A SER 3.3 0.2 - - - -
21A SER* 1.3 76.8 - - - +
23A THR* 1.3 55.7 + - - +
25A TYR* 3.8 2.1 - - - +
26A LEU* 2.8 41.8 + - + +
65A VAL* 3.6 20.0 - - - +
99A THR* 3.5 30.3 + - - +
162A ILE* 5.6 1.0 - - - +
165A TYR* 3.4 35.6 + - + +
7C A 3.4 30.5 + - - +
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Residues in contact with THR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.8 10.6 - - + +
6A ILE 4.9 0.2 - - - -
7A ASN* 3.4 30.9 + - + +
12A VAL* 3.9 20.6 - - + +
19A PRO 3.0 16.5 + - - -
20A SER 3.7 3.6 - - - -
21A SER 3.2 0.2 - - - -
22A GLU* 1.3 79.3 - - - +
24A ILE* 1.3 57.1 + - - +
26A LEU* 3.4 9.9 + - - +
27A PHE* 2.9 26.7 + - - +
39A ILE* 4.2 20.4 - - + -
65A VAL* 4.2 14.3 - - + +
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Residues in contact with ILE 24 (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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12A VAL* 3.9 14.1 - - + -
13A ILE 3.8 6.1 - - - +
14A ASN* 3.5 44.0 - - - +
15A PHE* 3.4 28.3 - - + +
20A SER* 3.0 13.9 + - - +
21A SER 3.8 2.5 - - - +
23A THR* 1.3 72.6 - - - +
25A TYR* 1.3 60.3 + - - +
27A PHE* 3.2 9.3 - - + +
28A LYS* 2.8 33.0 + - + +
39A ILE* 4.1 6.5 - - + -
47A TYR* 3.8 35.2 - - + -
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Residues in contact with TYR 25 (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 PHE* 3.5 36.1 - + - -
21A SER* 2.7 36.4 + - - +
22A GLU* 3.9 1.1 - - - +
24A ILE* 1.3 70.9 - - - +
26A LEU* 1.3 66.2 + - - +
28A LYS* 3.4 11.6 + - + +
29A VAL* 3.1 20.4 + - - +
165A TYR* 3.7 23.5 - + + -
166A LYS* 4.4 21.9 - - + -
169A MET* 3.2 40.6 - - + +
171A ASP* 5.7 4.5 - - - -
240A MET 5.9 0.2 - - - -
241A ASN* 3.7 29.7 + - + +
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Residues in contact with LEU 26 (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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5A ILE* 4.2 9.6 - - + -
22A GLU* 2.8 32.8 + - + +
23A THR 3.6 4.3 - - - +
25A TYR* 1.3 75.9 - - - +
27A PHE* 1.3 64.9 + - - +
29A VAL* 3.1 25.4 - - + +
30A ILE* 3.1 17.0 - - + +
65A VAL* 3.7 22.9 - - + -
97A LEU* 3.7 29.2 - - + -
99A THR* 6.0 0.9 - - + -
162A ILE* 4.0 16.6 - - + +
165A TYR* 3.5 33.9 - - + -
341A TRP* 6.2 0.7 - - + -
345A PHE* 6.3 3.4 - - + -
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Residues in contact with PHE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.6 4.4 - - + +
23A THR 2.9 14.4 + - - +
24A ILE* 3.2 11.2 - - + +
26A LEU* 1.3 77.6 - - - +
28A LYS* 1.3 68.8 + - + +
30A ILE* 3.3 9.8 + - - +
31A SER* 3.0 39.3 + - - -
37A VAL* 3.0 55.6 - - + -
38A ASP* 4.1 4.9 - - - -
39A ILE* 3.4 31.9 - - + -
47A TYR* 4.4 26.0 - + - -
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Residues in contact with LYS 28 (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 PHE* 3.7 20.4 - - + -
24A ILE* 2.8 23.1 + - + +
25A TYR* 3.9 16.8 - - + +
26A LEU 3.3 0.2 - - - -
27A PHE* 1.3 83.2 - - + +
29A VAL* 1.3 60.4 + - - +
31A SER* 3.2 6.8 + - - -
32A GLU* 2.9 42.9 + - + +
47A TYR* 3.5 39.7 + - - -
169A MET* 4.3 11.4 - - + -
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Residues in contact with VAL 29 (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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25A TYR 3.1 15.1 + - - +
26A LEU* 3.1 19.3 - - + +
28A LYS* 1.3 76.3 - - - +
30A ILE* 1.3 70.6 + - + +
32A GLU* 3.4 9.8 + - + +
33A MET* 3.3 24.5 + - + +
165A TYR* 4.1 23.3 - - + +
168A HIS* 4.5 12.8 - - + +
169A MET* 4.0 13.1 - - - -
338A LYS* 6.3 0.9 - - - -
341A TRP* 3.6 39.7 - - + -
342A GLN* 5.2 2.6 + - - +
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Residues in contact with ILE 30 (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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3A ILE* 4.3 7.6 - - + -
5A ILE* 4.5 13.2 - - + -
26A LEU* 3.1 24.1 + - + +
27A PHE* 3.6 8.1 - - - +
29A VAL* 1.3 81.7 - - + +
31A SER* 1.3 65.4 + - - +
33A MET* 3.0 23.6 + - + +
35A LEU* 3.5 35.4 + - + +
37A VAL* 4.1 21.1 - - + -
63A ILE* 4.5 12.3 - - + -
97A LEU* 6.4 0.7 - - + -
345A PHE* 3.8 34.1 - - + -
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Residues in contact with SER 31 (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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27A PHE* 3.0 27.4 + - - -
28A LYS* 3.2 11.9 + - - -
30A ILE* 1.3 76.2 - - - +
32A GLU* 1.3 55.5 - - - +
33A MET 3.0 0.2 - - - -
34A GLY* 2.7 27.9 + - - -
35A LEU 3.7 13.4 + - - +
37A VAL* 3.2 19.9 + - - +
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Residues in contact with GLU 32 (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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28A LYS* 2.9 29.0 + - + +
29A VAL* 3.7 10.1 - - + +
30A ILE 3.2 0.2 - - - -
31A SER* 1.3 76.1 - - - +
33A MET* 1.3 58.4 + - - +
34A GLY* 3.0 2.3 + - - -
168A HIS 4.3 2.1 - - - +
169A MET* 3.8 17.0 - - - +
170A ASN* 2.9 56.6 + - - +
171A ASP* 5.1 0.7 + - - +
338A LYS* 5.2 4.5 + - - +
342A GLN* 4.3 9.9 + - - +
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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