Contacts of the strand formed by residues 27 - 42 (chain G) in PDB entry 3U8M
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 VAL 27 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19G ILE* 3.6 35.5 - - + +
20G PRO* 3.7 39.5 - - + +
21G THR* 4.0 4.4 - - + +
22G GLN* 4.4 6.7 - - - +
25G ARG 3.7 0.2 + - - -
26G PRO* 1.3 74.5 - - - +
28G ALA* 1.3 69.0 + - - +
29G VAL* 3.3 23.4 + - + +
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Residues in contact with ALA 28 (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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22G GLN* 5.0 4.5 - - - +
26G PRO* 3.4 6.7 + - - +
27G VAL* 1.3 75.4 - - - +
29G VAL* 1.3 62.8 + - - +
30G SER* 4.0 1.7 + - - -
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Residues in contact with VAL 29 (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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27G VAL* 3.3 23.5 + - + +
28G ALA* 1.3 75.0 - - - +
30G SER* 1.3 69.9 + - - +
31G VAL* 4.0 17.5 + - + +
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Residues in contact with SER 30 (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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28G ALA 4.0 2.5 + - - -
29G VAL* 1.3 78.3 - - - +
31G VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 31 (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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29G VAL* 4.0 21.0 + - + +
30G SER* 1.3 79.2 - - - +
32G SER* 1.3 70.5 + - - +
33G LEU* 4.7 12.3 - - + -
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Residues in contact with SER 32 (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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31G VAL* 1.3 80.4 - - - +
33G LEU* 1.3 70.7 + - - +
34G LYS* 3.5 34.4 + - - +
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Residues in contact with LEU 33 (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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31G VAL* 4.7 13.5 - - + -
32G SER* 1.3 80.9 + - - +
34G LYS* 1.3 65.0 + - - +
35G PHE* 3.7 42.0 + - + -
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Residues in contact with LYS 34 (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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186F SER* 6.3 1.4 - - - -
187F CYS* 5.8 8.3 - - - +
32G SER* 3.5 28.5 + - - +
33G LEU* 1.3 75.3 - - - +
35G PHE* 1.3 64.7 + - - +
36G ILE* 3.5 20.6 - - + +
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Residues in contact with PHE 35 (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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33G LEU* 3.7 41.9 + - + -
34G LYS* 1.3 73.2 - - - +
36G ILE* 1.3 64.8 + - - +
37G ASN 5.0 7.4 - - - +
38G ILE* 5.7 12.8 - - + -
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Residues in contact with ILE 36 (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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89F TYR 4.6 14.8 - - - +
90F ASN* 5.9 2.0 - - - -
34G LYS* 3.5 24.2 - - + +
35G PHE* 1.3 79.6 - - - +
37G ASN* 1.3 72.6 + - + +
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Residues in contact with ASN 37 (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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92F ILE* 4.3 7.1 - - + +
122F SER* 3.0 37.0 + - - -
35G PHE* 3.8 6.2 - - - +
36G ILE* 1.3 89.6 + - + +
38G ILE* 1.3 85.9 + - - +
39G LEU* 3.6 24.5 + - + +
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Residues in contact with ILE 38 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35G PHE* 5.7 13.0 - - + -
37G ASN* 1.3 90.7 + - - +
39G LEU* 1.3 62.6 + - - +
40G GLU 4.8 1.3 - - - +
41G VAL* 3.7 28.7 - - + -
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Residues in contact with LEU 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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45F THR* 5.2 6.8 - - - +
47F GLU* 3.8 29.6 - - + +
92F ILE* 3.9 42.0 - - + +
120F ARG* 5.9 2.2 - - - +
37G ASN* 3.6 39.0 - - + +
38G ILE* 1.3 76.4 - - - +
40G GLU* 1.3 66.0 + - + +
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Residues in contact with GLU 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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38G ILE* 3.8 2.1 - - - +
39G LEU* 1.3 85.1 - - + +
41G VAL* 1.3 72.5 + - - +
42G ASN* 4.3 7.2 + - + +
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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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38G ILE* 3.7 29.2 - - + -
40G GLU* 1.3 81.2 - - - +
42G ASN* 1.3 72.7 + - - +
43G GLU 4.4 2.9 - - - +
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Residues in contact with ASN 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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40G GLU* 4.3 7.5 + - + +
41G VAL* 1.3 79.5 - - - +
43G GLU 1.3 51.2 + - - +
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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