Contacts of the strand formed by residues 58 - 63 (chain A) in PDB entry 5UU1
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 HIS 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TRP* 3.7 29.6 - + + -
45A LEU* 3.9 0.3 - - - -
46A ALA* 3.0 31.2 + - + +
48A PRO* 4.1 20.8 - - + +
56A ALA* 3.9 7.1 - - - +
57A ARG* 1.3 97.7 + - + +
59A VAL* 1.3 69.5 + - - +
104A TYR* 3.6 50.5 + + - -
120A VAL* 4.0 12.1 - - + -
121A MET 3.3 9.2 - - - +
123A ARG* 3.7 2.4 - - - +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 4.2 9.2 - - + -
43A ILE* 3.9 15.0 - - + -
44A TYR 3.1 15.3 - - - +
45A LEU* 4.2 3.6 - - + -
46A ALA* 4.1 2.7 - - - +
58A HIS* 1.3 77.1 - - - +
60A VAL* 1.3 65.0 + - - +
61A LYS 5.1 0.2 - - - +
120A VAL* 3.3 6.9 - - - +
121A MET* 2.8 43.3 + - + +
122A GLU 4.0 1.1 - - - +
123A ARG* 3.9 22.0 - - + +
401A 7DZ 3.3 47.6 - - + +
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.8 22.9 - - + -
29A TRP* 4.7 5.6 - - + -
31A LEU* 3.8 20.9 - - + -
42A LEU 3.3 5.2 - - - +
43A ILE* 3.4 2.1 - - - -
44A TYR* 2.9 31.7 + - + +
46A ALA* 3.6 22.2 - - + -
59A VAL* 1.3 76.9 - - - +
61A LYS* 1.3 59.9 + - - +
62A VAL* 3.4 26.2 - - + -
118A PHE* 3.9 10.8 - - + -
119A MET 3.3 3.4 - - - +
120A VAL* 4.0 19.5 - - + -
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLY 3.8 13.0 - - - -
40A PHE 5.2 3.1 - - - +
41A GLY* 4.4 10.3 - - - +
42A LEU 3.4 4.3 - - - -
43A ILE* 3.8 10.1 - - + -
59A VAL* 4.1 0.8 - - + -
60A VAL* 1.3 71.6 - - - +
62A VAL* 1.3 60.4 + - - +
70A LEU* 3.8 16.9 - - + +
73A GLU* 2.7 30.2 + - - +
118A PHE* 3.0 4.0 - - - -
119A MET* 2.8 47.3 + - + +
121A MET* 4.7 4.0 - - + -
186A ASP* 2.8 25.1 + - - -
401A 7DZ 3.0 49.4 + - + +
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 3.5 36.1 - - + -
21A LEU* 5.1 1.6 - - + -
31A LEU* 5.6 0.4 - - + -
41A GLY* 3.1 5.7 - - - -
42A LEU* 2.7 37.1 + - + +
44A TYR* 3.9 24.7 - - + -
60A VAL* 3.4 27.1 - - + -
61A LYS* 1.3 72.3 - - - +
63A GLU* 1.3 76.9 + - - +
70A LEU* 4.7 1.3 - - - -
109A THR* 3.9 13.2 - - + -
116A TYR* 3.9 2.0 - - + -
117A ARG 3.6 10.5 - - - +
118A PHE* 4.2 2.9 - - + +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 4.4 2.8 - - - -
40A PHE 3.9 13.0 - - - +
62A VAL* 1.3 87.9 - - - +
64A TYR* 1.3 60.1 + - - +
65A GLN* 3.6 12.6 - - + +
67A ASN 2.7 27.7 + - - +
68A GLY* 4.2 2.4 - - - -
69A PRO* 5.6 1.1 - - + -
70A LEU* 3.4 35.2 + - + +
115A SER 5.5 0.2 - - - +
116A TYR* 3.4 17.2 - - + +
117A ARG* 2.9 61.7 + - - +
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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