Contacts of the strand formed by residues 16 - 21 (chain P) in PDB entry 4PJO
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 ARG 16 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15P TYR* 1.3 72.6 - - - +
17P MET* 1.3 54.3 + - - +
28P ILE* 3.6 25.5 + - - +
29P GLY* 3.5 10.0 - - - -
30P THR* 3.1 25.8 + - - +
43P CYS 3.3 13.9 + - - -
44P ASP* 2.8 35.0 + - - +
46P ASP* 4.3 12.3 + - - +
82P VAL* 3.8 0.7 - - - -
83P GLU* 2.8 37.7 + - + +
84P GLY* 3.1 26.4 + - - +
85P PRO 4.2 11.5 + - - +
87P PRO* 4.3 13.9 - - + -
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Residues in contact with MET 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P HIS* 3.4 36.1 - - + +
15P TYR* 3.9 14.1 - - + +
16P ARG* 1.3 76.9 - - - +
18P ARG* 1.3 60.5 + - - +
19P CYS* 3.6 14.0 + - - -
27P PHE 3.3 6.1 - - - +
28P ILE* 4.2 3.3 - - - +
29P GLY 2.9 33.7 + - - +
31P PHE* 3.9 21.5 - - + -
42P LEU* 5.1 1.3 - - + +
80P MET* 4.1 18.4 - - + +
81P THR* 3.1 43.7 - - - +
82P VAL* 3.2 17.7 - - + +
57Q THR* 5.8 0.2 - - + -
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Residues in contact with ARG 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P MET* 1.3 70.5 - - - +
19P CYS* 1.3 59.1 + - - +
20P ILE* 4.0 11.8 + - + +
26P ILE* 3.4 42.5 - - + +
27P PHE 3.5 3.8 - - - -
28P ILE* 4.0 17.2 - - + +
62P GLU* 5.9 0.8 + - - -
79P SER 3.9 0.2 - - - +
80P MET* 3.4 2.5 - - - -
81P THR* 2.8 50.4 + - + +
83P GLU* 3.1 42.1 + - + +
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Residues in contact with CYS 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P MET* 3.7 15.7 - - - -
18P ARG* 1.3 76.0 - - - +
20P ILE* 1.3 61.9 + - - +
21P LEU* 3.8 4.7 - - + +
25P ARG 3.8 0.3 - - - +
26P ILE* 3.2 6.3 - - - -
27P PHE* 2.7 46.5 + - + +
40P LEU* 3.8 25.8 - - + -
42P LEU* 4.0 14.4 - - - -
72P LEU* 4.8 1.1 - - + -
77P LEU* 3.9 16.2 - - + -
79P SER 3.4 5.6 - - - -
80P MET* 4.2 12.8 - - - -
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Residues in contact with ILE 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P ARG* 4.1 18.6 - - - +
19P CYS* 1.3 74.6 - - - +
21P LEU* 1.3 72.9 + - - +
24P GLY* 5.0 7.0 - - - -
25P ARG 3.6 6.5 - - - +
26P ILE* 3.8 23.1 - - + -
77P LEU* 3.7 3.1 - - - +
78P VAL* 2.9 37.3 + - + +
79P SER* 2.9 37.4 + - - +
80P MET* 5.3 0.4 - - - -
81P THR* 5.5 2.9 - - + +
21Q ASN* 5.3 5.4 - - - +
45Q MET* 4.5 20.2 - - + -
47Q LEU* 5.1 17.7 - - + -
58Q LEU* 5.5 1.8 - - + -
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Residues in contact with LEU 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69O ARG* 5.4 4.3 - - - -
70O PHE* 5.4 2.7 - - + -
19P CYS* 3.8 17.9 - - + +
20P ILE* 1.3 91.3 - - - +
22P GLN* 1.3 66.8 + - - +
23P ASP* 3.2 15.3 - - - +
24P GLY* 3.1 11.1 + - - -
25P ARG* 3.0 26.9 + - + +
27P PHE* 3.7 43.1 - - + -
72P LEU* 4.0 31.9 - - + -
76P ASN* 3.2 16.6 - - + +
77P LEU* 4.7 0.9 - - + -
78P VAL* 3.8 3.9 - - - +
21Q ASN* 5.5 0.7 + - - -
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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