Contacts of the strand formed by residues 27 - 35 (chain l) in PDB entry 5MQF
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 l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1682 A 5.2 0.5 - - - +
20l CYS 3.4 6.5 - - - +
21l GLU* 4.6 5.8 - - + +
25l GLY 4.6 3.1 - - - +
26l GLU* 1.3 73.5 - - - +
28l TYR* 1.3 60.4 + - - +
29l ARG* 4.1 0.4 - - - +
47l THR 3.4 2.4 - - - +
48l VAL* 3.2 6.3 - - - -
49l THR* 2.9 51.8 + - - +
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Residues in contact with TYR 28 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18l VAL 3.8 1.6 - - - +
19l THR* 3.4 3.0 - - - -
20l CYS* 2.7 50.4 + - + +
26l GLU 5.4 1.3 - - - +
27l VAL* 1.3 71.8 - - - +
29l ARG* 1.3 59.4 + - - +
46l ILE* 5.3 8.3 - - + -
47l THR 3.6 4.5 - - - -
48l VAL* 4.5 7.4 - - + +
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Residues in contact with ARG 29 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1682 A 2.6 55.4 - - + +
18l VAL 3.4 7.6 - - - +
19l THR* 4.6 8.7 - - - -
27l VAL 4.0 0.9 + - - +
28l TYR* 1.3 73.6 - - - +
30l GLY* 1.3 58.3 + - - +
45l ASN 3.9 1.2 - - - +
46l ILE* 3.3 5.9 - - - +
47l THR* 2.9 37.1 + - - +
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Residues in contact with GLY 30 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1682 A 5.9 0.6 + - - -
17l ILE* 4.1 8.4 - - - +
18l VAL* 2.8 32.9 + - - +
28l TYR 4.3 0.2 + - - -
29l ARG* 1.3 75.1 - - - +
31l LYS* 1.3 63.6 + - - -
32l LEU 3.5 0.5 + - - -
43l MET* 5.0 6.6 - - - +
44l SER 3.9 9.6 - - - -
45l ASN 4.0 5.8 - - - -
46l ILE* 4.6 2.2 - - - -
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Residues in contact with LYS 31 (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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15l GLY* 5.4 5.6 - - - +
16l HIS 3.5 11.0 - - - +
17l ILE* 4.3 3.1 - - + +
30l GLY* 1.3 70.9 - - - -
32l LEU* 1.3 65.1 + - - +
33l ILE* 3.3 1.7 + - - +
43l MET* 3.1 7.6 - - - -
44l SER* 3.0 41.5 + - - +
45l ASN* 6.1 0.7 - - + -
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Residues in contact with LEU 32 (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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13l ALA* 4.0 14.1 - - + +
14l GLU* 3.5 5.1 - - - -
15l GLY* 2.6 34.1 + - - -
16l HIS 2.9 17.5 + - - +
18l VAL* 4.6 13.7 - - + -
30l GLY 3.5 2.6 + - - -
31l LYS* 1.3 71.2 - - - +
33l ILE* 1.3 59.5 + - - +
34l GLU 5.2 4.0 - - - +
35l ALA* 6.1 3.1 - - + -
42l GLN 3.9 4.9 - - - +
43l MET* 4.6 3.4 - - - +
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Residues in contact with ILE 33 (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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14l GLU* 4.0 12.3 - - - +
15l GLY* 4.7 1.1 + - - +
31l LYS* 3.3 5.1 + - - +
32l LEU* 1.3 74.9 - - - +
34l GLU* 1.3 61.1 + - + +
42l GLN* 2.8 26.7 + - + +
43l MET* 4.7 3.8 - - - +
44l SER* 5.4 4.7 - - - +
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Residues in contact with GLU 34 (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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8k GLU* 5.7 9.2 - - + -
14l GLU* 5.1 2.7 - - - -
32l LEU* 5.3 3.6 - - - +
33l ILE* 1.3 82.0 - - + +
35l ALA* 1.3 61.6 + - - +
36l GLU 4.2 0.9 - - - -
40l ASN 3.8 0.9 - - - +
41l CYS* 3.5 4.0 - - - +
42l GLN* 2.8 43.1 + - + +
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Residues in contact with ALA 35 (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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10l LEU* 4.6 24.7 - - + +
11l HIS* 4.8 16.3 - - + +
14l GLU* 5.2 7.0 - - + +
32l LEU* 6.1 3.8 - - + -
34l GLU* 1.3 75.1 - - - +
36l GLU* 1.3 65.2 + - - +
39l MET* 6.0 2.0 - - - -
40l ASN 3.4 5.6 - - - +
41l CYS* 4.8 3.8 - - + +
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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