Contacts of the strand formed by residues 54 - 64 (chain F) 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 ALA 54 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50F TYR* 3.7 3.8 - - - -
51F ILE* 2.9 23.6 + - - +
52F ASP* 3.1 10.6 + - - +
53F GLY* 1.3 76.9 - - - +
55F LEU* 1.3 67.8 + - - +
56F SER* 4.3 0.7 - - - -
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F GLU* 3.2 40.8 - - + +
49F GLU 4.1 2.0 - - - +
50F TYR* 3.4 34.2 - - + +
54F ALA* 1.3 74.7 - - - +
56F SER* 1.3 64.4 - - - +
57F GLY* 3.6 20.0 - - - +
58F HIS* 6.1 0.2 - - + -
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Residues in contact with SER 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F GLU* 2.7 35.3 + - - -
51F ILE* 4.0 29.4 - - - +
54F ALA 3.4 1.2 + - - -
55F LEU* 1.3 79.5 - - - +
57F GLY* 1.3 53.8 + - - +
42K ALA* 3.5 18.0 - - - +
43K PRO* 5.0 3.1 - - - +
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Residues in contact with GLY 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F GLU* 3.2 7.2 - - - +
49F GLU 2.9 25.8 + - - -
55F LEU* 3.6 12.5 - - - +
56F SER* 1.3 82.1 - - - +
58F HIS* 1.3 60.3 + - - -
59F LEU* 3.5 4.6 - - - +
42K ALA* 3.8 12.9 - - - +
45K ILE* 6.1 1.1 - - - -
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Residues in contact with HIS 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ASN* 3.5 38.0 + - - -
47F THR 4.0 12.1 - - - -
48F GLU* 4.0 23.1 - - + +
55F LEU* 6.1 0.2 - - + -
57F GLY* 1.3 71.0 - - - -
59F LEU* 1.3 69.8 + - - +
60F GLY* 4.1 10.8 - - - -
45K ILE* 3.4 26.7 - - - +
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Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D LEU* 3.9 20.9 - - + -
113D PRO* 3.3 26.3 - - - +
29F TYR* 3.3 39.7 - - + -
47F THR* 2.9 12.0 + - + +
48F GLU 4.6 1.6 - - - -
49F GLU* 3.7 18.8 - - + +
57F GLY 3.5 16.8 - - - +
58F HIS* 1.3 89.8 + - - +
60F GLY* 1.3 58.8 + - - +
62F VAL* 4.3 11.0 - - + -
41K ILE* 4.0 24.2 - - + -
42K ALA* 4.2 15.0 - - + -
45K ILE* 4.7 4.6 - - + +
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Residues in contact with GLY 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D LEU* 3.8 5.6 - - - -
113D PRO* 4.6 8.1 - - - -
46F ASN* 3.7 7.0 + - - -
47F THR* 2.7 45.0 + - - +
58F HIS* 4.1 7.5 - - - -
59F LEU* 1.3 80.9 - - - +
61F GLU* 1.3 58.6 + - - -
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Residues in contact with GLU 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D SER* 4.8 1.2 + - - -
31D VAL* 3.9 15.8 + - + +
34D GLN* 5.6 3.3 - - - +
109D VAL 4.1 0.2 - - - +
110D LEU* 3.4 6.4 - - - +
111D ARG* 3.2 65.3 + - + +
113D PRO* 5.7 0.4 - - - +
43F GLN* 3.0 29.5 + - - +
44F LEU 3.5 9.9 - - - +
45F ALA* 4.5 7.9 - - + +
60F GLY* 1.3 70.7 - - - -
62F VAL* 1.3 61.1 + - - +
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Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D VAL* 4.4 4.0 - - - -
108D VAL* 4.0 13.2 - - + -
109D VAL 3.3 6.5 - - - +
110D LEU* 3.8 20.4 - - + -
29F TYR* 5.0 3.4 - - + -
42F MET 3.5 0.9 - - - +
43F GLN* 3.3 4.2 - - - -
44F LEU* 2.8 36.2 + - + +
47F THR* 3.8 24.7 - - + +
59F LEU* 4.3 11.9 - - + -
60F GLY 3.7 10.3 - - - +
61F GLU* 1.3 79.7 - - - +
63F LEU* 1.3 77.4 + - - +
64F ILE* 3.8 17.2 - - + +
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Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D PRO* 3.7 31.9 - - + +
29D LEU* 4.2 13.0 - - + -
31D VAL* 4.0 15.6 - - + +
32D LEU* 4.1 27.4 - - + -
63D CYS* 4.0 26.2 - - - -
106D VAL* 6.2 0.2 - - + -
108D VAL* 3.4 5.2 - - - -
109D VAL* 2.9 47.1 + - + +
41F ASN* 4.5 4.0 - - + -
42F MET 3.5 8.3 - - - +
62F VAL* 1.3 76.6 - - - +
64F ILE* 1.3 75.4 + - - +
65F ARG* 4.6 1.6 - - + +
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Residues in contact with ILE 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ILE 3.9 8.5 - - - +
108D VAL* 3.9 8.5 - - + -
21F VAL* 4.0 31.2 - - + -
23F LEU* 4.3 14.4 - - + -
29F TYR* 4.3 14.4 - - + -
41F ASN* 3.6 4.0 - - - +
42F MET* 2.7 38.6 + - + +
44F LEU* 4.1 23.3 - - + -
62F VAL* 3.8 12.3 - - + +
63F LEU* 1.3 79.7 - - - +
65F ARG* 1.3 77.0 + - - +
66F CYS* 3.3 2.1 + - - -
68F ASN* 4.7 0.4 - - + -
69F VAL* 4.0 19.5 - - + +
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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