Contacts of the strand formed by residues 38 - 50 (chain l) in PDB entry 5Z58
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 GLN 38 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106H G 4.3 14.1 - - - +
35l LEU* 3.6 23.9 + - + +
36l TYR 2.9 7.1 + - - +
37l GLU* 1.3 79.1 - - - +
39l VAL* 1.3 60.5 + - - +
40l ASN 3.6 1.6 - - - +
41l MET* 3.2 25.3 - - + +
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Residues in contact with VAL 39 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37l GLU 4.2 1.0 - - - -
38l GLN* 1.3 71.6 - - - +
40l ASN* 1.3 65.2 + - - +
41l MET* 3.2 7.1 + - - +
42l ARG* 5.6 1.4 - - - +
66l SER* 4.3 10.4 - - - -
23n GLY* 5.3 10.8 - - - +
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Residues in contact with ASN 40 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38l GLN* 4.6 0.8 - - + +
39l VAL* 1.3 77.9 - - - +
41l MET* 1.3 57.8 + - + +
64l ILE 4.3 0.2 - - - -
65l HIS* 3.4 8.0 - - - +
66l SER* 3.0 32.2 + - - -
67l LYS* 4.3 16.3 + - + +
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Residues in contact with MET 41 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35l LEU* 4.1 10.9 + - - +
38l GLN* 3.2 28.0 + - + +
39l VAL 4.2 3.5 - - - +
40l ASN* 1.3 82.4 - - + +
42l ARG* 1.3 62.6 + - - +
63l GLU* 5.6 5.6 - - + -
64l ILE 3.3 10.5 - - - +
65l HIS* 5.2 2.0 - - + -
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Residues in contact with ARG 42 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32l GLN* 5.9 3.6 - - + -
33l VAL 3.3 17.9 - - - +
34l TRP* 4.8 4.7 - - - -
35l LEU* 5.2 3.1 - - - +
39l VAL 5.6 1.1 - - - +
41l MET* 1.3 76.2 - - - +
43l ILE* 1.3 60.8 + - - +
63l GLU* 3.6 2.9 - - - +
64l ILE* 2.7 48.3 + - + +
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Residues in contact with ILE 43 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32l GLN* 3.5 3.3 - - - +
33l VAL* 2.7 50.2 + - + +
35l LEU* 5.9 1.0 - - - +
42l ARG* 1.3 75.2 - - - +
44l GLU* 1.3 62.9 + - - +
61l ALA* 6.3 0.7 - - + -
62l GLU 3.4 7.0 - - - +
63l GLU* 4.8 1.3 - - - +
64l ILE* 5.8 0.4 - - - -
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Residues in contact with GLU 44 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31l ILE 3.1 12.3 - - - +
32l GLN* 4.7 6.7 - - + -
43l ILE* 1.3 76.2 - - - +
45l GLY* 1.3 58.6 + - - +
58l LEU* 4.8 2.3 - - - +
60l ASP 5.1 0.4 - - - -
61l ALA* 3.0 27.3 - - - +
62l GLU* 2.9 26.3 + - + +
64l ILE* 5.8 5.4 - - + -
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Residues in contact with GLY 45 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30l ARG* 4.5 5.7 - - - +
31l ILE* 2.7 43.6 + - - +
44l GLU* 1.3 76.5 - - - +
46l CYS* 1.3 58.7 + - - -
47l ILE 3.8 0.6 + - - -
58l LEU* 4.2 11.0 - - - -
59l ASP 3.5 13.0 - - - -
60l ASP 4.4 2.7 - - - -
61l ALA* 4.1 3.4 - - - -
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Residues in contact with CYS 46 (chain l).
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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28l ARG* 4.8 14.6 - - + +
29l SER 4.1 14.4 - - - +
30l ARG* 4.8 4.0 - - + +
45l GLY* 1.3 71.1 - - - -
47l ILE* 1.3 67.7 + - - +
48l ILE* 3.1 3.5 + - - +
58l LEU* 4.1 1.8 - - - -
59l ASP* 2.9 46.0 + - + +
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Residues in contact with ILE 47 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21l ILE 5.6 0.4 - - - +
24l TYR* 4.7 10.1 - - + +
25l LEU* 3.7 38.8 - - + +
28l ARG* 5.3 2.8 - - - +
29l SER 4.6 4.6 + - - +
31l ILE* 5.2 7.4 - - + +
45l GLY 3.8 4.2 + - - -
46l CYS* 1.3 70.9 - - - +
48l ILE* 1.3 59.9 + - - +
49l GLY 4.8 6.3 - - - +
50l PHE* 6.2 2.0 - - + -
56l LEU* 5.8 6.7 - - + -
57l VAL 3.4 10.1 - - - +
58l LEU* 4.6 1.9 - - - +
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Residues in contact with ILE 48 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25l LEU* 5.1 6.6 - - - +
46l CYS 3.1 5.0 + - - +
47l ILE* 1.3 74.6 - - - +
49l GLY* 1.3 58.8 + - - +
57l VAL* 2.9 15.6 + - + +
58l LEU 5.7 0.2 - - - -
59l ASP* 5.4 7.9 - - + +
2m SER* 4.6 16.2 - - - +
4m PRO* 3.6 9.4 - - - +
5m LEU* 3.2 35.8 + - + +
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Residues in contact with GLY 49 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25l LEU* 5.6 5.2 - - - -
47l ILE* 3.6 5.3 - - - +
48l ILE* 1.3 81.9 + - - +
50l PHE* 1.3 64.5 + - - +
56l LEU* 3.7 0.9 - - - +
57l VAL 2.8 26.9 + - - +
4m PRO* 5.1 4.0 - - - -
5m LEU 3.0 22.2 + - - -
6m ASN* 4.2 3.4 - - - -
7m PRO 4.8 0.2 - - - -
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Residues in contact with PHE 50 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21l ILE* 6.0 6.5 - - + -
47l ILE* 6.2 2.0 - - + -
49l GLY* 1.3 76.7 - - - +
51l ASP* 1.3 65.4 + - - +
54l MET* 5.1 3.8 - - - -
55l ASN 3.2 16.4 - - - +
56l LEU* 4.3 5.2 - - + -
6m ASN* 4.3 12.4 - - - +
7m PRO 4.8 6.3 - - - -
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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