Contacts of the helix formed by residues 91 - 102 (chain N) in PDB entry 5DM6
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 ASN 91 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90N LEU* 1.3 72.4 - - - +
92N ARG* 1.3 53.8 + - - +
93N LYS* 3.8 14.5 - - - +
94N VAL* 3.5 21.1 - - + +
95N LEU* 2.7 31.7 + - - +
11O GLN* 2.4 49.5 + - - +
996X A 2.7 65.6 + - - +
997X G 3.1 7.3 + - - +
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Residues in contact with ARG 92 (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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58N ARG* 3.0 35.5 - - - +
61N TRP* 3.4 17.3 - - + +
62N ILE* 3.9 10.7 - - - +
65N ILE* 3.5 20.1 - - + +
76N TYR* 3.0 14.3 + - - -
80N ILE* 4.0 14.0 - - + +
84N LYS* 5.6 0.4 - - - +
90N LEU 3.6 1.6 + - - -
91N ASN* 1.3 70.5 - - - +
93N LYS* 1.3 64.4 + - - +
95N LEU* 3.6 12.3 - - + -
96N ALA* 2.8 29.8 + - - +
996X A 4.4 1.1 - - - +
997X G 2.9 35.8 + - - +
998X C 2.9 30.3 + - - -
1153X C 2.7 29.1 + - - -
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Residues in contact with LYS 93 (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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30G LYS* 3.8 31.1 - - - +
31G THR* 4.3 9.3 - - + +
61N TRP* 3.6 36.3 - - + +
91N ASN* 3.8 16.8 - - - +
92N ARG* 1.3 83.3 - - - +
94N VAL* 1.3 61.8 + - + +
96N ALA* 3.3 4.0 - - - +
97N ASP* 3.0 26.9 + - + +
11O GLN 5.2 5.2 - - - +
995X C 3.2 55.7 + - - +
996X A 3.5 16.4 + - - +
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Residues in contact with VAL 94 (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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90N LEU* 4.4 20.0 - - + -
91N ASN* 3.3 29.3 + - + +
92N ARG 3.2 0.2 - - - -
93N LYS* 1.3 79.3 - - + +
95N LEU* 1.3 59.9 + - - +
97N ASP* 3.1 8.1 + - + +
98N ILE* 2.9 50.0 + - + +
11O GLN* 3.5 24.7 - - + +
12O TYR 4.9 10.3 - - - +
13O ARG* 5.5 8.3 - - + +
39O PHE* 6.1 1.8 - - + -
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Residues in contact with LEU 95 (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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65N ILE* 3.8 17.5 - - + -
79N PHE* 4.6 13.2 - - + -
80N ILE* 5.0 11.9 - - + -
83N LEU* 3.7 33.0 - - + -
90N LEU* 3.7 37.7 - - + +
91N ASN 2.7 27.4 + - - +
92N ARG* 3.7 13.9 - - + +
93N LYS 3.3 0.2 - - - -
94N VAL* 1.3 70.3 - - - +
96N ALA* 1.3 64.5 + - - +
98N ILE* 3.5 5.0 + - + +
99N ALA* 2.9 24.9 + - - +
106N PHE* 3.9 6.8 - - + -
109N LEU* 4.1 11.4 - - + -
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Residues in contact with ALA 96 (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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31G THR* 5.7 1.1 - - + -
61N TRP* 3.8 35.4 - - + +
64N ARG* 4.4 16.5 + - + +
65N ILE* 3.9 8.5 - - - +
92N ARG 2.8 18.4 + - - +
93N LYS 3.3 5.8 - - - +
95N LEU* 1.3 76.7 - - - +
97N ASP* 1.3 57.4 - - - +
99N ALA* 3.0 8.0 + - - +
100N ALA* 2.9 30.5 + - - +
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Residues in contact with ASP 97 (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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30G LYS 4.8 7.8 - - - +
31G THR* 5.5 6.7 - - + +
32G TYR* 3.9 19.6 - - - +
64N ARG* 5.7 1.6 - - - +
93N LYS* 3.0 14.0 + - + +
94N VAL* 3.1 10.3 + - + +
96N ALA* 1.3 72.5 - - - +
98N ILE* 1.3 66.0 + - + +
100N ALA* 4.5 2.5 - - - +
101N ARG* 2.9 73.9 + - - +
102N GLU* 5.4 0.2 - - - -
13O ARG* 3.9 19.3 - - - +
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Residues in contact with ILE 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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90N LEU* 5.5 2.0 - - + -
94N VAL* 2.9 38.3 + - + +
95N LEU* 3.7 8.7 - - + +
97N ASP* 1.3 75.8 - - + +
99N ALA* 1.3 59.7 + - - +
102N GLU* 2.8 46.9 + - + +
105N ALA* 4.1 12.1 - - + -
106N PHE* 3.8 31.2 - - + +
109N LEU* 4.5 14.4 - - + -
13O ARG* 5.8 8.1 - - - +
39O PHE* 3.8 31.6 - - + -
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Residues in contact with ALA 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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68G PRO* 3.6 17.9 - - + +
64N ARG 4.6 15.5 - - - +
65N ILE* 4.7 2.2 - - - -
68N GLY* 4.9 4.2 - - - -
95N LEU 2.9 15.3 + - - +
96N ALA* 3.1 13.0 - - - +
98N ILE* 1.3 77.2 - - - +
100N ALA* 1.3 58.4 + - - +
102N GLU 5.0 2.6 + - - +
103N PRO* 5.3 3.5 - - - +
106N PHE* 3.3 37.8 - - + +
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Residues in contact with ALA 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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32G TYR* 3.9 23.6 - - + -
68G PRO* 4.0 18.9 - - - +
69G ASP* 4.2 7.1 - - - +
64N ARG* 3.9 22.7 - - - +
96N ALA 2.9 14.1 + - - +
97N ASP* 4.2 3.8 - - - +
99N ALA* 1.3 77.4 - - - +
101N ARG* 1.3 63.7 + - + +
103N PRO* 5.3 2.5 - - - +
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Residues in contact with ARG 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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30G LYS 4.9 9.3 + - - -
32G TYR* 4.2 33.5 - - + +
97N ASP* 2.9 56.5 + - - +
100N ALA* 1.3 79.9 - - - +
102N GLU* 1.3 79.4 + - - +
103N PRO* 3.2 11.0 - - - +
13O ARG* 4.2 24.9 - - - +
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Residues in contact with GLU 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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97N ASP 4.7 1.7 - - - +
98N ILE* 2.8 33.9 + - + +
99N ALA 5.2 0.4 - - - -
101N ARG* 1.3 95.9 - - - +
103N PRO* 1.3 66.5 - - + +
104N GLU 3.7 1.3 - - - -
105N ALA* 3.5 17.6 + - + +
106N PHE* 3.1 16.1 + - - +
13O ARG* 3.6 30.9 + - - -
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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