Contacts of the helix formed by residues 3 - 20 (chain A) in PDB entry 5XJY
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 CYS 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A TRP* 1.3 70.4 + - - +
5A PRO* 3.7 10.5 - - - +
6A GLN* 3.5 34.3 + - - +
7A LEU* 4.0 7.1 + - - +
680A ILE* 4.9 4.6 - - + +
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Residues in contact with TRP 4 (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 CYS* 1.3 77.7 - - - +
5A PRO* 1.3 80.7 - - + +
7A LEU* 2.6 36.6 + - + +
8A ARG* 2.9 48.5 + - + +
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Residues in contact with PRO 5 (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 CYS* 3.7 8.1 - - - +
4A TRP* 1.3 113.5 - - + +
6A GLN* 1.3 59.4 + - + +
7A LEU 3.2 0.2 - - - -
8A ARG* 3.6 7.1 - - + +
9A LEU* 2.9 29.8 + - - +
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Residues in contact with GLN 6 (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 CYS* 3.5 37.7 + - - +
4A TRP 3.0 0.2 + - - -
5A PRO* 1.3 82.6 - - + +
7A LEU* 1.3 60.0 + - - +
9A LEU* 3.8 4.0 - - - +
10A LEU* 2.8 31.1 + - - +
676A LEU* 3.3 35.3 - - + +
680A ILE* 4.7 18.1 - - + +
999A ARG 6.0 1.1 - - - -
1000A LEU* 5.6 11.9 - - - +
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Residues in contact with LEU 7 (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 CYS 4.1 5.2 - - - +
4A TRP* 2.6 22.0 + - + +
6A GLN* 1.3 75.4 - - - +
8A ARG* 1.3 58.1 + - - -
10A LEU* 3.8 2.0 - - + -
11A LEU* 2.9 50.3 + - + +
680A ILE* 3.7 35.9 - - + +
683A PHE* 3.7 31.6 - - + -
684A SER* 3.9 19.3 - - - -
687A ILE* 6.0 0.2 - - + -
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Residues in contact with ARG 8 (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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4A TRP* 2.9 53.4 + - + +
5A PRO* 4.0 9.9 - - + +
6A GLN 3.4 0.2 - - - -
7A LEU* 1.3 77.0 - - - +
9A LEU* 1.3 56.6 + - - +
11A LEU* 3.4 27.2 + - - +
12A TRP* 2.9 32.9 + - - +
15A LEU* 5.0 12.4 - - - +
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Residues in contact with LEU 9 (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 PRO 2.9 18.4 + - - +
6A GLN* 4.3 4.7 - - - +
8A ARG* 1.3 75.6 - - - +
10A LEU* 1.3 59.8 + - - +
12A TRP* 3.0 30.4 + - + +
13A LYS* 2.9 24.8 + - - +
995A TRP* 5.2 2.2 - - + +
996A PHE* 3.6 39.5 - - + +
999A ARG* 3.7 27.4 - - + -
1000A LEU* 3.8 10.8 - - + +
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Residues in contact with LEU 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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6A GLN 2.8 19.2 + - - +
7A LEU* 3.7 6.7 - - + +
8A ARG 3.2 0.2 - - - -
9A LEU* 1.3 78.2 - - - +
11A LEU* 1.3 56.5 + - - +
13A LYS* 3.0 38.0 + - + +
14A ASN* 3.0 28.8 + - - +
671A MET* 4.9 9.9 - - + -
676A LEU* 5.0 6.3 - - + -
680A ILE* 3.4 50.5 - - + +
681A LEU* 4.3 13.0 - - + -
684A SER* 3.4 17.0 - - - +
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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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7A LEU* 2.9 43.4 + - + +
8A ARG* 3.7 25.1 - - - +
10A LEU* 1.3 73.6 - - - +
12A TRP* 1.3 61.3 + - - +
14A ASN* 3.8 4.9 - - - +
15A LEU* 2.9 46.2 + - + +
684A SER* 3.4 28.7 - - - +
687A ILE* 4.2 26.2 - - + -
688A SER* 4.9 7.0 - - - -
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Residues in contact with TRP 12 (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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8A ARG* 2.9 24.2 + - - +
9A LEU* 3.0 33.8 + - + +
11A LEU* 1.3 75.6 - - - +
13A LYS* 1.3 54.3 + - - +
15A LEU* 4.9 2.7 - - + -
16A THR* 2.2 72.7 + - + +
19A ARG* 3.8 33.2 - - - -
992A GLU* 4.7 18.0 - - + +
996A PHE* 5.7 5.8 - - + -
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Residues in contact with LYS 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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9A LEU 2.9 10.8 + - - +
10A LEU* 3.0 28.2 + - + +
12A TRP* 1.3 80.2 - - - +
14A ASN* 1.3 71.5 + - - +
16A THR* 3.8 2.3 - - - -
17A PHE* 3.0 63.8 + - + -
662A GLU* 4.9 11.5 + - - +
667A LEU* 5.1 11.0 + - + +
671A MET* 3.4 31.2 - - + +
681A LEU* 4.6 9.3 - - - +
685A TRP* 4.9 8.1 - - - +
985A PHE* 5.6 7.4 - - + -
988A LEU* 6.4 0.7 - - + -
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Residues in contact with ASN 14 (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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10A LEU* 3.0 15.4 + - - +
11A LEU* 4.2 2.2 - - - +
13A LYS* 1.3 82.5 - - - +
15A LEU* 1.3 63.5 + - - +
17A PHE* 3.3 21.5 - - - +
18A ARG* 3.5 15.4 + - - +
684A SER* 2.3 48.3 + - - -
685A TRP* 3.2 45.0 - - + +
688A SER* 3.6 20.8 - - - +
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Residues in contact with LEU 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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8A ARG* 5.0 12.6 - - - +
11A LEU* 2.9 33.9 + - + +
12A TRP* 4.7 3.1 - - + +
14A ASN* 1.3 78.0 - - - +
16A THR* 1.3 58.0 + - - +
18A ARG* 3.1 12.6 + - + +
19A ARG* 2.9 31.9 + - - +
688A SER* 3.4 25.6 - - - +
691A ILE* 5.8 9.2 - - + -
692A PRO* 5.9 2.5 - - + -
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Residues in contact with THR 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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12A TRP* 2.2 68.2 + - + +
13A LYS* 4.0 2.5 - - - -
15A LEU* 1.3 74.3 - - - +
17A PHE* 1.3 67.8 + - - +
19A ARG* 4.1 14.1 + - + +
20A ARG* 3.0 42.2 + - + +
987A MET 5.2 0.8 - - - +
988A LEU* 4.7 17.0 - - + +
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Residues in contact with PHE 17 (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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13A LYS* 3.0 49.8 + - + -
14A ASN* 3.3 12.6 - - - +
16A THR* 1.3 77.6 - - - +
18A ARG* 1.3 65.2 + - - +
20A ARG* 4.1 3.0 + - - +
21A GLN* 3.3 31.1 + - - +
658A GLY* 6.0 1.6 - - - -
661A TYR* 5.9 10.1 - + - -
662A GLU* 5.2 8.3 - - + -
667A LEU* 4.6 15.7 - - + -
685A TRP* 4.1 28.7 - + - -
985A PHE* 4.8 18.4 - - + -
986A ASP 5.1 1.8 - - - -
987A MET* 5.2 12.1 - - + -
988A LEU* 5.2 9.9 - - + -
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Residues in contact with ARG 18 (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* 3.5 14.7 + - - +
15A LEU* 3.1 14.0 + - + +
17A PHE* 1.3 83.3 - - - +
19A ARG* 1.3 64.5 - - - +
20A ARG 3.2 1.6 - - - -
21A GLN* 3.2 22.3 + - - +
22A THR 3.5 7.3 + - - -
24A GLN* 5.9 1.3 - - + -
25A LEU* 3.3 47.8 - - + +
654A VAL* 3.9 30.2 + - + +
655A ILE* 3.4 34.4 - - - +
658A GLY* 5.8 2.4 - - - -
685A TRP* 5.2 7.8 - - - -
688A SER* 3.6 29.7 + - - -
689A SER* 5.3 0.6 - - - +
692A PRO* 4.5 13.1 - - - +
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Residues in contact with ARG 19 (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 TRP* 3.8 33.4 - - - -
15A LEU* 2.9 20.8 + - - +
16A THR* 3.3 15.2 + - + +
18A ARG* 1.3 76.3 - - - +
20A ARG* 1.3 83.8 + - - +
21A GLN 3.4 3.1 + - - -
22A THR* 3.4 20.0 - - - +
25A LEU* 4.4 5.6 - - - +
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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 THR* 3.0 29.8 + - + +
17A PHE* 4.6 2.5 - - - +
18A ARG 3.2 0.4 - - - -
19A ARG* 1.3 104.9 + - - +
21A GLN* 1.3 62.0 + - - +
22A THR* 4.8 0.9 - - - -
987A MET* 3.9 18.3 - - + +
988A LEU 3.8 23.8 - - - +
989A THR* 6.0 0.4 - - - -
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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
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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