Contacts of the strand formed by residues 74 - 78 (chain A) in PDB entry 5DQZ
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 LEU 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA 3.1 14.8 + - - +
51A CYS* 3.4 20.1 - - - -
52A ILE 2.8 27.4 + - - +
72A GLY 3.8 3.0 + - - +
73A THR* 1.3 70.7 - - - +
75A LEU* 1.3 65.1 + - - +
76A VAL* 3.7 14.6 - - + -
88A SER* 3.9 8.1 - - - +
89A GLY 3.5 24.9 - - - +
90A GLN* 3.4 28.5 - - + +
196A LEU* 3.6 29.4 - - + +
197A ALA* 4.2 4.3 - - - +
86B TYR* 3.7 1.8 - - - -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 6.3 2.5 - - + -
32A PHE* 5.5 1.8 - - + -
52A ILE* 3.5 39.9 - - + +
54A LEU* 4.7 7.6 - - + -
60A VAL* 4.5 8.3 - - + -
64A ALA* 5.6 0.7 - - + -
65A VAL* 4.3 21.8 - - + -
68A ALA* 4.4 19.7 - - + -
73A THR* 4.7 1.1 - - + -
74A LEU* 1.3 75.6 - - - +
76A VAL* 1.3 60.8 + - - +
77A TRP* 3.8 33.4 - - + -
88A SER* 3.7 0.2 - - - -
89A GLY 2.7 31.5 + - - -
86B TYR* 3.0 28.3 + - + +
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A CYS* 3.9 13.5 - - - -
52A ILE 2.9 8.9 + - - -
53A MET* 3.5 18.1 - - + -
54A LEU* 2.9 26.5 + - - +
74A LEU* 3.7 28.3 - - + -
75A LEU* 1.3 79.7 - - - +
77A TRP* 1.3 63.0 + - - +
78A VAL* 3.4 21.1 + - + +
85A VAL* 4.4 14.1 - - + -
87A ALA 3.6 12.1 - - - +
88A SER* 4.7 3.8 - - - +
193A ALA* 5.5 2.7 - - - -
196A LEU* 4.5 15.5 - - + -
197A ALA 5.9 0.2 - - - +
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Residues in contact with TRP 77 (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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54A LEU* 3.4 30.1 - - + +
58A THR* 5.2 0.6 + - - -
60A VAL* 3.9 18.0 - - + +
75A LEU* 3.8 40.2 - - + -
76A VAL* 1.3 71.5 - - - +
78A VAL* 1.3 55.6 + - - +
85A VAL* 4.1 0.3 - - - +
86A TYR* 2.9 36.6 + - + +
87A ALA* 2.8 36.0 + - + +
89A GLY* 3.9 10.8 - - - -
62B HIS* 3.8 35.9 - + + +
65B VAL* 3.6 43.3 - - + +
66B ARG 5.5 0.7 - - - +
77B TRP* 4.0 23.6 - + - -
86B TYR* 4.9 1.6 - + - -
88B SER* 4.1 11.4 - - - -
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Residues in contact with VAL 78 (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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19A PHE* 4.6 0.4 - - + -
53A MET* 4.0 24.5 - - + -
54A LEU 3.0 27.1 + - - +
55A GLU* 4.1 5.8 - - + +
56A PRO* 3.2 4.9 - - - +
76A VAL* 3.6 26.9 - - + +
77A TRP* 1.3 78.4 - - - +
79A GLY* 1.3 75.0 + - - +
82A GLY* 4.1 14.1 - - - +
84A ARG 3.2 13.2 - - - +
85A VAL* 4.2 10.8 - - + -
86A TYR* 3.8 4.9 - - - -
193A ALA* 5.0 2.2 - - + -
62B HIS* 2.8 26.0 + - - -
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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