Contacts of the helix formed by residues 102 - 107 (chain N) in PDB entry 5D4D
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 ILE 102 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100N ALA 3.4 4.3 + - - -
101N HIS* 1.3 72.6 + - - +
103N TRP* 1.3 62.4 + - + +
105N VAL* 3.5 10.1 - - + -
106N LYS* 2.8 45.5 + - + +
107N ASP 4.1 0.9 + - - -
128N TYR* 4.7 3.1 - - - +
575N GLN* 6.0 0.2 - - - +
579N ASP* 3.6 31.1 + - + +
582N LEU* 4.2 11.1 - - + +
583N ASP* 3.7 33.9 - - + +
586N ARG* 3.6 24.6 - - + +
587N ARG* 3.5 32.8 - - + +
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Residues in contact with TRP 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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1095M LEU* 3.7 27.1 - - + +
1097M LEU* 3.6 32.5 - - + -
101N HIS* 3.0 26.8 + + + +
102N ILE* 1.3 78.9 - - + +
104N PHE* 1.3 63.5 + + + +
107N ASP* 3.2 28.8 - - - +
111N LYS* 5.6 0.9 - - - +
582N LEU 5.8 0.2 - - - -
583N ASP* 3.6 20.2 + - + -
586N ARG* 6.1 0.4 - - + -
604N THR* 3.0 33.2 + - + -
607N LEU* 4.6 3.8 - - + -
1443N THR* 5.9 0.7 - - + -
1444N THR* 3.4 36.2 + - + +
1447N LEU* 3.8 31.0 - - + -
1448N THR* 3.5 29.3 - - + +
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Residues in contact with PHE 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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1097M LEU* 4.3 16.8 - - + -
12N LEU* 3.6 27.6 - - + -
101N HIS* 2.9 47.9 + + + +
103N TRP* 1.3 80.1 - + + +
105N VAL* 1.3 60.1 + - - +
107N ASP 5.1 0.4 - - - -
110N SER* 3.1 16.6 + - - -
111N LYS* 3.7 10.7 + - + -
112N ILE* 3.5 20.8 + - + +
512N MET* 3.8 36.1 - - + -
1448N THR* 4.1 24.9 - - + -
1451N ALA* 4.8 3.1 - - + -
1452N ILE* 3.9 28.3 - - + -
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Residues in contact with VAL 105 (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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100N ALA* 3.8 14.4 - - + -
101N HIS 3.6 13.7 - - - +
102N ILE* 3.0 13.1 + - + +
103N TRP 3.2 0.2 - - - -
104N PHE* 1.3 82.5 - - - +
106N LYS* 1.3 80.4 + - + +
107N ASP 3.3 1.5 - - - -
108N VAL* 5.6 0.9 - - - +
110N SER* 3.3 24.6 - - - -
112N ILE* 4.1 9.0 - - + -
123N LEU* 4.5 12.2 - - + +
124N GLU* 5.9 2.0 - - - +
127N LEU* 3.6 34.5 - - + -
128N TYR* 5.0 8.7 - - + +
575N GLN* 5.6 0.4 - - - +
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Residues in contact with LYS 106 (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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102N ILE* 2.8 40.7 + - + +
105N VAL* 1.3 86.9 - - + +
107N ASP* 1.3 60.0 + - - +
108N VAL* 3.4 13.2 + - - +
124N GLU* 4.2 13.9 - - + +
128N TYR* 6.1 0.2 - - + -
586N ARG* 3.1 40.3 + - + +
587N ARG* 3.6 29.5 - - + +
10R C 3.5 23.3 + - - -
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Residues in contact with ASP 107 (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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102N ILE 4.1 0.8 + - - -
103N TRP* 3.2 22.0 + - - +
104N PHE 5.4 0.5 - - - -
105N VAL 3.3 1.4 - - - -
106N LYS* 1.3 77.5 - - - +
108N VAL* 1.3 60.7 + - - +
109N PRO 3.3 17.3 - - - +
110N SER* 3.5 6.7 + - - -
111N LYS* 4.6 10.0 + - - +
586N ARG* 4.7 5.4 - - - +
1444N THR* 4.6 11.7 - - + +
1445N HIS* 3.1 41.7 + - - +
1448N THR* 3.5 17.4 + - - -
11R G 5.8 0.3 + - - -
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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