Contacts of the strand formed by residues 38 - 48 (chain G) in PDB entry 5M64
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 ILE 38 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D HIS* 3.8 9.3 - - - -
31D VAL* 3.5 18.0 - - - +
32D SER 4.8 3.1 - - - +
33D THR* 6.2 3.6 - - + -
36D VAL* 5.5 8.7 - - + -
96D PHE* 5.6 3.1 - - + -
35G SER 5.3 1.1 - - - +
36G ASN* 3.6 3.3 - - - +
37G CYS* 1.3 86.3 - - - +
39G VAL* 1.3 65.4 + - - +
40G ARG* 4.8 20.4 - - - +
82G LEU* 4.3 21.1 - - + -
123G TYR* 5.5 0.9 - - + -
124G VAL 3.9 7.6 - - - +
125G TRP* 3.6 25.6 - - + +
150G HIS* 4.2 25.1 - - + +
153G PHE* 6.2 0.2 - - + -
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Residues in contact with VAL 39 (chain G).
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* 4.4 14.6 - - + +
29D GLN 4.0 5.4 - - - +
30D HIS* 3.7 38.8 - - + +
31D VAL* 4.6 1.1 - - - -
24G VAL* 5.2 7.2 - - + -
26G ASN* 4.9 1.8 - - - +
37G CYS 3.6 1.6 + - - +
38G ILE* 1.3 74.3 - - - +
40G ARG* 1.3 74.0 + - - +
41G VAL* 3.6 22.7 - - + -
123G TYR* 3.8 1.4 - - - +
124G VAL* 2.7 33.7 + - + +
126G GLN* 3.3 34.8 - - - +
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Residues in contact with ARG 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLN 4.0 16.4 + - - +
31D VAL* 3.3 44.0 - - + +
32D SER 4.6 3.6 + - - -
35D GLU* 4.0 4.6 - - - +
36D VAL* 3.7 33.9 - - - +
39D PHE* 3.3 34.2 - - - -
38G ILE* 4.8 12.4 - - - +
39G VAL* 1.3 82.7 - - - +
41G VAL* 1.3 62.9 + - - +
42G PRO* 3.6 8.0 - - - +
121G ASN* 3.5 14.6 + - - +
122G LEU 3.7 5.4 - - - -
123G TYR* 3.2 56.4 - - + +
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Residues in contact with VAL 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ALA* 4.4 10.3 - - + -
26D GLN 4.8 1.1 - - - +
28D PRO* 3.6 37.7 - - + -
39G VAL* 3.6 21.3 + - + -
40G ARG* 1.3 70.3 - - - +
42G PRO* 1.3 77.6 - - + +
43G ILE* 3.6 11.1 + - + +
77G VAL* 3.8 24.5 - - + -
121G ASN* 3.2 3.6 - - - -
122G LEU* 2.9 32.6 + - - +
124G VAL* 3.7 12.3 - - + +
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Residues in contact with PRO 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D THR* 2.8 31.8 + - + +
26D GLN* 3.8 37.3 + - + +
27D LEU 4.8 0.7 - - - +
28D PRO* 4.6 10.8 - - + -
29D GLN 5.2 1.3 - - - +
40G ARG 3.6 8.5 - - - +
41G VAL* 1.3 90.6 - - + +
43G ILE* 1.3 60.9 + - - +
119G HIS* 6.3 2.9 - - + -
120G VAL 4.7 0.9 - - - +
121G ASN* 3.7 29.6 - - + +
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Residues in contact with ILE 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.7 27.4 - - + -
23D HIS 3.7 2.9 - - - +
24D ALA* 3.8 18.2 - - + +
25D THR* 3.2 6.6 + - - -
41G VAL* 4.2 14.8 - - + +
42G PRO* 1.3 78.8 - - - +
44G ALA* 1.3 58.8 + - - +
45G LEU* 4.3 9.2 - - + -
76G LYS* 6.4 1.6 - - + -
77G VAL* 5.1 11.9 - - + -
119G HIS* 3.4 1.2 - - - +
120G VAL* 2.8 56.9 + - + +
122G LEU* 3.8 28.7 - - + -
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Residues in contact with ALA 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.2 6.7 - - - +
23D HIS 2.7 33.8 + - - +
25D THR* 3.3 6.4 + - + +
58F PHE* 3.5 32.8 - - + -
43G ILE* 1.3 70.9 - - - +
45G LEU* 1.3 59.3 + - - +
46G TYR* 3.6 16.9 - - + +
118G CYS 5.0 0.9 - - - +
119G HIS* 4.0 14.6 - - + +
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Residues in contact with LEU 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PRO* 3.8 26.2 - - + -
22D ILE* 3.9 16.8 - - + -
43G ILE* 3.8 14.5 + - + -
44G ALA* 1.3 72.3 - - - +
46G TYR* 1.3 61.3 + - - +
47G VAL* 3.5 35.3 + - + -
61G VAL* 4.8 6.7 - - + -
65G HIS* 5.3 8.7 - - + +
66G LEU* 6.0 5.6 - - + -
69G LEU* 5.7 7.9 - - + -
117G TRP 3.9 0.2 - - - -
118G CYS* 2.8 51.0 + - - +
120G VAL* 4.5 9.9 - - + -
122G LEU* 6.0 1.3 - - + -
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Residues in contact with TYR 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202B PRO* 3.9 15.7 - - + -
1203B LYS* 3.5 21.1 + - - -
19D PRO* 3.3 17.9 - - - +
20D VAL* 3.5 15.7 + - + +
21D VAL* 3.0 45.0 + - + +
23D HIS* 4.7 4.9 - + - -
58F PHE* 3.2 29.3 - + - -
62F GLU* 4.8 3.5 + - - -
65F ARG* 5.4 3.4 + - - -
44G ALA* 3.6 25.9 - - + +
45G LEU* 1.3 70.7 - - - +
47G VAL* 1.3 59.6 + - - +
116G THR 3.9 4.0 - - - -
117G TRP* 3.3 54.1 - + + +
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Residues in contact with VAL 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PRO* 4.3 8.5 - - + -
20D VAL* 5.4 2.7 - - - +
45G LEU* 3.5 19.5 + - + -
46G TYR* 1.3 74.1 - - - +
48G SER* 1.3 77.0 + - - +
61G VAL* 3.6 19.1 - - + -
65G HIS* 3.3 48.7 - - + +
115G PHE* 3.8 4.4 - - - +
116G THR* 2.8 50.3 + - + +
117G TRP* 4.9 0.5 - - - -
118G CYS* 4.8 3.4 - - - -
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Residues in contact with SER 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PRO* 6.1 0.7 - - - +
8A GLY* 6.1 0.3 - - - -
15D THR* 4.5 15.4 + - - -
16D LEU* 6.3 1.3 - - - -
20D VAL* 6.0 2.1 - - - +
47G VAL* 1.3 95.7 - - - +
49G LEU* 1.3 75.2 + - - +
61G VAL* 4.6 2.4 - - - +
65G HIS* 4.6 11.3 - - - -
113G PHE* 4.3 12.3 - - - -
114G GLY 3.1 13.2 - - - -
115G PHE* 3.2 27.4 - - - -
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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