Contacts of the strand formed by residues 56 - 65 (chain s) 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 LEU 56 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21s ILE* 4.9 5.6 - - + -
33s VAL* 4.0 26.5 - - + -
47s ILE* 4.4 18.6 - - + -
49s GLY 3.6 3.4 - - - +
50s PHE* 3.8 16.4 - - + -
54s MET* 3.6 22.7 - - + +
55s ASN* 1.3 75.8 - - - +
57s VAL* 1.3 63.2 + - - +
58s LEU* 4.0 25.6 + - + +
77s ILE 3.6 0.9 - - - +
78s MET* 3.2 5.8 - - - +
79s LEU* 2.9 40.5 + - + +
84s ILE* 4.0 15.5 - - + -
87s LEU* 4.2 11.7 - - + -
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Residues in contact with VAL 57 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47s ILE* 3.5 4.7 - - - -
48s ILE* 3.0 31.2 + - + -
49s GLY 2.8 18.2 + - - +
56s LEU* 1.3 74.4 - - - +
58s LEU* 1.3 61.6 + - - +
76s ARG* 4.2 15.5 - - + -
77s ILE 3.3 9.6 - - - +
78s MET* 4.5 2.5 - - + -
5t LEU* 3.2 29.2 - - + +
6t ASN 3.5 22.9 - - - +
7t PRO* 3.5 12.1 - - + -
10t PHE* 4.0 24.5 - - + -
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Residues in contact with LEU 58 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31s ILE* 5.2 3.1 - - + +
33s VAL* 5.0 5.4 - - + -
43s ILE* 3.9 28.0 - - + -
44s GLU 5.0 0.2 - - - -
45s GLY* 4.0 22.2 - - - +
46s CYS 3.3 2.9 - - - +
47s ILE* 3.7 29.8 - - + -
48s ILE* 3.8 2.5 - - - -
56s LEU* 4.2 21.5 - - + +
57s VAL* 1.3 75.2 - - - +
59s ASP* 1.4 62.5 + - - +
60s ASP 3.7 0.7 - - - -
61s ALA* 4.0 8.3 - - + -
75s GLY 3.7 2.9 - - - +
76s ARG* 3.4 1.9 - - - +
77s ILE* 2.8 50.0 + - + -
79s LEU* 4.5 14.1 - - + -
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Residues in contact with ASP 59 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46s CYS* 2.7 21.4 + - + +
48s ILE* 2.6 25.7 - - + +
58s LEU* 1.4 71.8 - - - +
60s ASP* 1.3 70.3 + - + +
61s ALA 3.6 0.7 - - - -
75s GLY 3.3 13.7 - - - +
76s ARG* 2.3 46.5 + - - +
2t SER* 5.5 1.6 - - - -
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Residues in contact with ASP 60 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30s ARG* 2.7 42.6 + - - +
45s GLY* 4.0 4.0 - - - -
46s CYS* 4.1 8.6 - - + +
59s ASP* 1.3 86.4 - - + +
61s ALA* 1.3 58.9 + - - +
62s GLU* 3.9 1.7 - - - +
75s GLY* 3.9 10.3 + - - -
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Residues in contact with ALA 61 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43s ILE* 4.8 0.9 - - + -
44s GLU 3.1 10.8 - - - +
45s GLY* 4.1 0.9 - - - -
58s LEU* 4.0 12.6 - - + -
60s ASP* 1.3 76.5 - - - +
62s GLU* 1.3 62.8 + - - +
73s GLN* 3.9 2.1 - - - +
74s LEU* 2.9 27.2 + - + +
75s GLY 3.0 20.1 + - - +
77s ILE* 3.6 37.7 - - + -
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Residues in contact with GLU 62 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30s ARG* 3.2 29.2 + - - +
43s ILE* 3.4 3.8 - - - +
44s GLU* 2.8 33.6 + - + +
60s ASP 3.9 1.6 - - - +
61s ALA* 1.3 75.5 - - - +
63s GLU* 1.3 63.6 - - - +
64s ILE* 4.0 3.4 + - + +
71s ARG* 2.9 46.3 + - + +
72s LYS 3.1 15.0 - - - +
73s GLN* 3.1 25.8 + - - +
74s LEU* 3.6 5.4 - - - -
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Residues in contact with GLU 63 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41s MET* 3.4 19.5 - - - +
42s ARG 3.5 6.1 - - - -
43s ILE* 4.2 7.4 - - + -
62s GLU* 1.3 72.8 - - - +
64s ILE* 1.3 59.7 + - - +
65s HIS* 3.3 35.9 + - + +
70s SER 4.1 1.0 - - - +
71s ARG* 3.5 3.1 - - - -
72s LYS* 2.9 39.3 + - + +
74s LEU* 3.7 15.5 - - + +
22t LYS* 3.9 13.3 + - - +
71t TYR* 2.7 34.9 + - - -
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Residues in contact with ILE 64 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32s GLN* 3.2 18.8 - - - +
40s ASN 3.8 0.7 - - - +
41s MET* 3.4 2.1 - - - -
42s ARG* 2.9 39.1 + - + +
43s ILE 4.5 2.7 - - - -
44s GLU* 3.2 41.7 - - + +
62s GLU* 4.1 8.1 - - + +
63s GLU* 1.3 77.1 - - - +
65s HIS* 1.3 68.7 + - - +
69s LYS* 5.8 4.9 - - + -
70s SER 4.2 4.9 - - - +
71s ARG* 3.6 37.5 - - + +
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Residues in contact with HIS 65 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40s ASN* 3.6 5.8 - - + +
41s MET* 3.9 24.1 - - + -
63s GLU* 3.3 45.2 + - + +
64s ILE* 1.3 80.0 - - - +
66s SER* 1.3 65.3 + - - +
67s LYS* 3.4 3.4 - - + +
68s THR* 3.8 25.2 - - + +
69s LYS* 3.2 23.4 + - - +
70s SER 3.7 12.9 + - - -
72s LYS* 4.2 16.8 - - + +
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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