Contacts of the strand formed by residues 97 - 104 (chain N) 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 LYS 97 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86N GLU* 3.5 26.2 + - + -
87N VAL 3.4 12.1 - - - +
88N TYR* 2.8 45.3 + - + -
89N PHE* 3.6 8.1 - - - -
95N PRO* 3.4 15.4 + - - +
96N ARG* 1.3 86.5 - - + +
98N VAL* 1.3 66.5 + - - +
99N ARG* 5.3 2.0 - - + +
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Residues in contact with VAL 98 (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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85N ILE 3.7 0.7 - - - +
86N GLU* 3.3 5.2 - - - +
87N VAL* 2.9 44.0 + - + +
89N PHE* 3.6 24.9 - - + -
97N LYS* 1.3 77.4 - - - +
99N ARG* 1.3 64.7 + - - +
100N PHE* 3.6 40.2 - - + -
122N LEU* 3.8 17.7 - - + -
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Residues in contact with ARG 99 (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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84N PRO* 3.3 28.1 - - + +
85N ILE 3.3 9.4 - - - +
86N GLU* 4.0 21.7 + - + +
97N LYS* 5.8 2.7 - - + -
98N VAL* 1.3 80.0 - - - +
100N PHE* 1.3 71.5 + - - +
101N ASP* 2.3 41.4 + - - -
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Residues in contact with PHE 100 (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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11N LEU* 5.3 4.9 - - + -
13N LEU* 4.0 34.1 - - + -
84N PRO* 3.4 3.5 - - - +
85N ILE* 2.8 40.5 + - + +
87N VAL* 4.7 9.6 - - + -
98N VAL* 3.6 42.0 - - + -
99N ARG* 1.3 79.4 - - - +
101N ASP* 1.3 64.4 + - - +
102N TYR 3.6 1.9 + - - +
118N ARG* 3.7 23.1 - - - +
120N GLU* 3.6 37.9 - - + -
121N LYS 5.6 0.9 - - - -
122N LEU* 3.9 14.6 - - + -
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Residues in contact with ASP 101 (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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82N ILE* 3.9 21.9 - - + +
83N LEU 4.2 2.2 - - - -
84N PRO* 4.0 5.8 - - - +
99N ARG* 2.3 40.5 + - - +
100N PHE* 1.3 70.2 - - - +
102N TYR* 1.3 63.1 + - - +
103N ASP* 3.4 3.6 + - - +
118N ARG* 3.2 18.9 + - - +
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Residues in contact with TYR 102 (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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13N LEU* 3.8 20.5 + - + -
14N GLY* 3.1 34.9 - - - -
15N HIS* 2.9 35.5 + + - -
34N VAL* 3.5 23.8 - - + -
35N PHE 5.0 0.2 - - - -
82N ILE* 4.7 1.1 - - - -
83N LEU* 2.7 49.9 + - + +
85N ILE* 3.8 19.1 - - + -
100N PHE 3.6 1.8 + - - -
101N ASP* 1.3 71.2 - - - +
103N ASP* 1.3 89.9 + - - +
104N LEU* 3.3 3.0 + - + -
116N HIS* 3.6 24.7 + + - -
118N ARG* 4.0 17.7 - - + +
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Residues in contact with ASP 103 (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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17J ARG* 3.4 28.3 + - - -
15N HIS* 3.9 2.6 - - - -
81N PHE 3.7 5.4 - - - +
82N ILE* 3.9 16.5 - - + +
101N ASP 3.4 5.8 + - - +
102N TYR* 1.3 89.7 - - + +
104N LEU* 1.3 75.2 + - - +
105N PHE* 3.2 23.6 + - - +
116N HIS* 5.5 0.5 - - - -
118N ARG* 4.8 1.4 - - - +
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Residues in contact with LEU 104 (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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17J ARG* 4.0 3.6 - - - +
15N HIS* 3.9 14.1 - - + -
32N TRP* 3.4 70.4 - - + +
34N VAL* 3.9 11.0 - - + -
80N GLY* 3.8 8.7 - - - -
81N PHE* 3.1 41.4 + - + +
83N LEU* 3.6 21.3 - - + -
102N TYR* 3.3 7.3 + - + +
103N ASP* 1.3 76.0 - - - +
105N PHE* 1.3 75.3 + - - +
106N LEU* 4.0 6.2 + - + -
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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