Contacts of the strand formed by residues 48 - 54 (chain A) in PDB entry 5HJD
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 5.2 1.1 - - + -
44A ILE* 2.8 36.6 + - + +
45A GLN* 3.3 15.8 - - - +
47A PHE* 1.3 95.3 - - + +
49A GLU* 1.3 63.7 + - - +
50A LYS 3.8 11.7 - - - +
51A VAL* 3.8 18.4 - - + -
67A LYS 5.4 0.3 - - - +
71A TYR* 3.7 31.0 + - + +
87A VAL* 3.8 19.7 - - + -
88A TYR 3.5 7.4 - - - +
89A PHE* 5.2 0.2 - - + -
90A LYS* 3.3 6.4 - - - -
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Residues in contact with GLU 49 (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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48A VAL* 1.3 75.4 - - - +
50A LYS* 1.3 75.4 + - + +
67A LYS* 3.2 21.8 - - - +
71A TYR* 5.4 0.2 - - - -
88A TYR* 2.9 24.9 + - - +
89A PHE 3.7 14.6 - - - +
90A LYS* 3.7 27.1 - - + +
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Residues in contact with LYS 50 (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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48A VAL* 3.6 3.7 - - - +
49A GLU* 1.3 93.9 + - + +
51A VAL* 1.3 65.5 + - - +
52A VAL* 4.3 10.5 - - + -
63A LYS* 5.8 3.8 - - - +
65A VAL* 4.4 15.3 - - + -
66A CYS 3.3 16.2 - - - +
67A LYS* 4.5 19.1 - - + +
71A TYR* 4.8 0.9 - - - -
88A TYR* 2.9 71.9 + - + +
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Residues in contact with VAL 51 (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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36A VAL* 4.2 11.0 - - + -
48A VAL* 3.8 12.8 - - + -
50A LYS* 1.3 77.0 - - - +
52A VAL* 1.3 64.1 + - - +
53A PHE* 3.7 29.8 + - + -
64A ARG 3.9 0.9 - - - +
65A VAL* 3.8 1.0 - - - -
66A CYS* 2.9 34.0 + - + +
71A TYR* 3.5 34.7 - - + -
85A ILE* 3.8 19.7 - - + -
86A GLU 3.5 4.0 - - - +
87A VAL* 4.2 16.6 - - + -
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Residues in contact with VAL 52 (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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50A LYS* 4.3 11.4 - - - -
51A VAL* 1.3 77.2 - - - +
53A PHE* 1.3 62.5 + - - +
54A HIS* 3.5 32.4 + - + +
63A LYS* 3.8 25.4 - - + +
64A ARG 3.4 9.2 - - - +
65A VAL* 3.9 22.0 - - + -
84A PRO 3.7 1.7 - - - +
85A ILE* 3.5 3.5 - - - -
86A GLU* 2.9 42.6 + - + +
88A TYR* 4.0 20.0 - - + +
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Residues in contact with PHE 53 (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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34A VAL* 3.9 24.2 - - + -
35A PHE 4.4 2.2 - - - -
36A VAL* 4.1 11.0 - - + -
51A VAL* 3.7 23.6 - - + -
52A VAL* 1.3 72.9 - - - +
54A HIS* 1.3 60.4 + - - +
55A LEU* 3.5 4.4 + - + -
62A PRO 3.3 2.6 - - - +
63A LYS* 3.7 1.2 - - - -
64A ARG* 2.9 40.0 + - + +
66A CYS* 4.0 15.0 - - - -
71A TYR 3.3 33.9 - - - -
72A LYS* 4.0 4.7 - - - -
73A VAL* 3.5 27.8 - - + -
83A LEU* 3.7 11.7 - - + -
84A PRO 4.0 0.7 - - - -
85A ILE* 3.9 32.1 - - + +
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Residues in contact with HIS 54 (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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52A VAL* 3.5 26.4 + - + +
53A PHE* 1.3 69.4 - - - +
55A LEU* 1.3 67.8 + - - +
62A PRO 3.7 3.1 - - - -
63A LYS* 4.0 27.0 - - + -
82A ILE 4.5 0.5 - - - +
83A LEU* 3.4 9.0 - - - +
84A PRO* 2.9 64.6 + - + +
86A GLU* 3.3 37.2 + - + -
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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