Contacts of the helix formed by residues 90 - 99 (chain C) in PDB entry 1AM4
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 THR 90 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ALA 3.4 8.0 + - - +
89C ASN* 1.3 71.7 + - - +
91C GLN* 1.3 85.3 + - - +
93C VAL* 4.1 6.0 - - - +
94C ARG* 3.4 22.5 + - - +
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Residues in contact with GLN 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ASN* 3.2 10.1 + - - +
90C THR* 1.3 98.7 + - - +
92C VAL* 1.3 67.2 + - + +
94C ARG* 2.9 12.1 + - - +
95C GLU* 3.3 13.6 + - - +
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ASN* 3.1 31.4 + - - +
91C GLN* 1.3 73.8 - - + +
93C VAL* 1.3 50.7 + - - +
95C GLU* 2.4 39.9 + - - +
96C VAL* 2.8 24.9 + - + -
111C TYR* 3.2 42.2 - - + -
112C ASN 5.7 2.2 - - - +
113C GLU* 5.1 3.1 - - + -
116C LEU* 3.8 13.0 - - + -
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ALA* 3.7 19.5 - - + +
89C ASN 2.8 23.7 + - - +
90C THR* 4.4 5.8 - - - +
91C GLN 3.2 0.2 + - - -
92C VAL* 1.3 70.9 - - - +
94C ARG* 1.3 62.5 + - + +
95C GLU 3.1 0.9 + - - -
96C VAL* 3.5 3.0 + - - -
97C GLN* 3.1 38.2 + - - +
116C LEU* 3.8 9.0 - - + -
119C VAL* 3.5 28.5 - - + -
120C ILE* 3.3 23.6 - - + +
123C THR* 4.6 7.4 - - + +
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Residues in contact with ARG 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PRO* 4.7 26.0 + - - -
37C ARG* 3.9 27.5 - - - +
90C THR 3.4 11.4 + - - +
91C GLN* 2.9 14.8 + - - +
93C VAL* 1.3 73.3 - - + +
95C GLU* 1.3 56.9 + - - +
97C GLN* 3.6 21.7 + - - +
98C GLN* 3.0 48.0 + - - +
127C GLU* 4.8 4.2 + - - -
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLN* 3.3 8.3 + - - +
92C VAL* 2.4 44.3 + - + +
94C ARG* 1.3 68.0 - - - +
96C VAL* 1.3 70.0 - - - +
97C GLN 2.9 0.7 - - - -
98C GLN* 2.8 18.3 + - + +
99C LYS* 3.0 18.7 + - + +
111C TYR* 3.9 24.1 + - - +
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C VAL* 2.8 24.8 + - + +
93C VAL* 4.1 5.2 - - - +
95C GLU* 1.3 79.4 - - - +
97C GLN* 1.3 57.6 - - - +
99C LYS* 2.9 24.4 + - - +
100C TYR* 3.3 24.2 + - + -
106C VAL* 3.2 32.5 - - + -
108C PHE* 3.6 12.3 - - + -
111C TYR* 4.5 10.9 + - + -
116C LEU* 3.7 35.0 - - + -
120C ILE* 4.1 12.8 - - + -
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Residues in contact with GLN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ARG* 2.7 40.1 + - - +
45C PHE* 3.4 32.3 - - + -
93C VAL* 3.1 25.9 + - - +
94C ARG* 3.6 25.2 + - - +
95C GLU 2.9 0.4 - - - -
96C VAL* 1.3 78.5 - - - +
98C GLN* 1.3 53.9 + - + +
100C TYR 4.1 2.9 - - - -
101C ASN* 2.6 33.1 + - - +
120C ILE* 4.6 3.1 - - + -
123C THR* 2.8 30.8 - - + +
127C GLU* 3.0 4.0 - - - +
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Residues in contact with GLN 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PRO* 3.8 31.1 + - - +
37C ARG* 5.0 9.2 - - + -
40C LEU* 4.6 3.8 - - + +
94C ARG* 3.0 33.9 + - + +
95C GLU* 2.8 11.7 + - - +
97C GLN* 1.3 80.1 - - + +
99C LYS* 1.3 62.6 + - - +
101C ASN* 3.4 21.3 - - - +
102C MET* 3.4 20.6 + - - +
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Residues in contact with LYS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLU* 3.0 12.9 + - + +
96C VAL* 2.9 14.1 - - - +
98C GLN* 1.3 75.5 - - - +
100C TYR* 1.3 55.2 + - - +
102C MET* 3.9 11.8 + - - -
103C GLY 3.6 1.9 + - - -
104C LEU* 2.8 66.6 + - + +
105C PRO 3.6 16.6 + - - +
106C VAL* 4.0 13.7 - - + -
110C GLN* 3.1 25.9 + - - +
111C TYR* 2.3 38.0 + - - +
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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