Contacts of the strand formed by residues 58 - 65 (chain N) in PDB entry 5U0A
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 LYS 58 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56N GLU* 3.8 17.2 + - - +
57N LEU* 1.3 79.0 - - - +
59N PHE* 1.3 61.8 + - - +
60N THR* 3.9 7.2 - - + +
116N ALA 3.5 2.4 - - - +
117N VAL* 3.3 6.4 - - - -
118N THR* 2.9 52.4 + - - +
119N GLY* 5.7 0.8 - - - -
187N GLU* 3.7 12.6 - - + +
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Residues in contact with PHE 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ARG* 4.0 40.6 - - + -
35N LEU* 3.5 24.2 - - + -
36N ILE* 4.3 11.4 - - + -
39N PHE* 3.8 22.7 - + - -
57N LEU* 3.7 27.1 - - + -
58N LYS* 1.3 73.1 - - - +
60N THR* 1.3 62.7 + - - +
61N VAL* 3.8 8.8 + - + +
115N VAL* 3.5 26.9 - - + -
116N ALA 4.4 0.2 - - - -
117N VAL* 3.7 22.7 - - + -
185N ILE* 3.5 9.9 - - - +
186N TYR 4.9 0.2 - - - -
187N GLU* 3.3 23.4 + - - +
217N ARG* 5.5 7.5 + - - +
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Residues in contact with THR 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N LYS* 5.4 5.2 - - + -
59N PHE* 1.3 74.8 - - - +
61N VAL* 1.3 59.8 + - - +
62N ARG 4.2 0.4 - - - -
115N VAL* 3.4 0.7 - - - -
116N ALA* 2.8 43.2 + - - +
159N VAL* 3.5 26.5 - - + +
162N LEU* 3.6 10.3 - - - +
184N LEU* 4.7 0.9 - - - -
185N ILE 3.1 5.4 - - - -
186N TYR* 3.5 36.8 - - + -
187N GLU* 5.4 2.0 - - + +
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Residues in contact with VAL 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N PRO* 3.8 27.4 - - + +
35N LEU* 5.6 0.7 - - + -
59N PHE* 3.8 13.0 - - + +
60N THR* 1.3 76.7 - - - +
62N ARG* 1.3 60.5 + - - +
63N VAL* 3.9 0.8 + - + -
113N PHE* 3.6 34.1 - - + -
114N THR 4.0 2.5 - - - -
115N VAL* 3.5 29.6 - - + -
184N LEU* 3.7 1.3 - - - -
185N ILE* 2.8 54.0 + - + +
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Residues in contact with ARG 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N THR 4.2 0.8 + - - -
61N VAL* 1.3 73.0 - - - +
63N VAL* 1.3 63.1 + - - +
64N ASP* 2.7 29.7 + - - -
113N PHE* 3.5 2.8 - - - -
114N THR* 2.8 63.6 + - - +
162N LEU* 3.5 45.5 + - + +
166N VAL* 3.1 36.3 + - - +
167N PRO 3.5 12.1 + - - -
168N LEU* 3.4 23.9 - - - +
182N VAL* 4.1 15.4 - - + +
183N ASP 3.3 9.6 - - - +
184N LEU* 3.8 20.1 - - + +
226N VAL* 6.3 0.4 - - - +
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Residues in contact with VAL 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N TYR* 5.1 2.7 - - + -
61N VAL 4.4 1.3 - - - +
62N ARG* 1.3 69.4 - - - +
64N ASP* 1.3 70.9 + - - +
66N PRO* 5.1 15.0 - - + -
113N PHE* 3.4 35.9 - - + -
171N ARG* 4.8 0.9 + - - -
182N VAL* 4.0 12.5 - - - +
183N ASP* 3.0 37.3 + - + +
185N ILE* 4.2 23.1 - - + -
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Residues in contact with ASP 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N ARG* 2.7 46.6 + - - +
63N VAL* 1.3 80.3 - - - +
65N ARG* 1.3 61.5 + - - +
66N PRO* 3.7 6.6 - - - +
112N VAL* 2.9 25.2 + - + +
114N THR* 4.0 12.7 - - - +
167N PRO 4.5 1.4 - - - +
168N LEU* 4.5 1.3 - - - +
169N PRO* 3.6 26.3 - - + +
171N ARG* 3.7 20.7 + - - +
238N TYR* 3.7 16.6 + - - -
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Residues in contact with ARG 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D TYR* 6.0 1.2 - - - -
31D GLY* 5.3 2.4 - - - -
32D GLY* 5.4 1.8 - - - +
301D GLU* 4.0 25.5 + - - +
63N VAL 4.8 1.1 - - - -
64N ASP* 1.3 81.0 - - + +
66N PRO* 1.3 71.4 - - + +
67N GLY* 3.0 3.6 + - - +
110N ASP* 3.3 44.7 + - - +
111N ALA* 3.5 1.6 - - - +
112N VAL* 3.3 42.1 + - + +
113N PHE* 4.8 2.4 - - - -
169N PRO* 4.5 25.5 - - + +
170N HIS 5.8 3.8 + - - +
238N TYR* 5.3 7.3 - - - -
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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