Contacts of the helix formed by residues 95 - 105 (chain C) in PDB entry 4U7D
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 LEU 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C PRO* 3.6 34.5 - - + -
93C ARG 3.4 0.2 + - - -
94C PRO* 1.3 72.4 - - + +
96C GLN* 1.3 61.3 + - - +
98C GLU* 2.8 36.2 + - + +
99C THR* 2.6 37.3 + - - +
111C LEU* 4.4 8.3 - - + -
113C MET* 4.4 2.7 - - + -
122C CYS* 5.2 0.2 - - - -
277C PHE* 4.1 12.8 - - + -
278C THR 3.1 16.8 - - - +
279C ALA* 3.1 42.4 - - + +
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Residues in contact with GLN 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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91C LYS 4.5 1.6 - - - +
92C PHE* 3.5 16.2 - - + -
93C ARG* 2.6 51.6 + - + +
94C PRO 3.0 7.5 + - - +
95C LEU* 1.3 76.8 - - - +
97C LEU* 1.3 63.8 + - - +
99C THR* 4.0 1.0 - - - -
100C ILE* 3.1 32.1 + - + +
113C MET* 4.5 5.6 - - + -
117C GLY 3.9 2.8 + - - -
118C GLY* 2.8 35.8 + - - +
121C LEU* 3.8 25.9 - - - +
122C CYS* 3.8 19.9 - - - -
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Residues in contact with LEU 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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69C ASN* 3.8 17.9 - - - +
70C LYS 3.8 21.3 - - - +
71C GLU* 3.9 23.8 - - + +
79C VAL* 5.2 6.5 - - + -
92C PHE* 4.1 38.9 - - + +
93C ARG 4.2 0.2 + - - -
95C LEU 3.2 0.2 - - - -
96C GLN* 1.3 79.5 - - - +
98C GLU* 1.3 69.6 + - - +
100C ILE* 3.2 5.7 + - + +
101C ASN* 2.9 46.9 + - - +
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Residues in contact with GLU 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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65C PRO* 3.2 32.0 - - + +
68C TRP* 3.5 13.8 - - + +
69C ASN* 3.4 38.2 + - - +
93C ARG 4.9 0.2 - - - +
94C PRO* 5.3 0.3 - - - +
95C LEU* 2.8 46.7 + - + +
97C LEU* 1.3 80.2 + - - +
99C THR* 1.3 60.7 + - - +
101C ASN* 3.5 2.4 + - - +
102C VAL* 3.3 27.7 + - - +
277C PHE* 4.0 12.1 - - + -
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Residues in contact with THR 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 LEU* 2.6 22.9 + - - +
96C GLN 4.0 2.5 - - - -
98C GLU* 1.3 75.4 - - - +
100C ILE* 1.3 64.4 + - - +
102C VAL* 3.3 5.1 + - - +
103C THR* 3.0 25.8 + - - -
109C VAL* 4.3 13.9 - - + +
111C LEU* 3.8 26.5 - - + +
122C CYS* 4.0 15.3 - - + -
251C ILE* 3.8 27.6 - - + -
277C PHE* 3.7 18.6 - - - -
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Residues in contact with ILE 100 (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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75C TRP* 5.3 0.2 - - - +
79C VAL* 4.4 13.9 - - + -
92C PHE* 3.7 26.2 - - + -
96C GLN* 3.1 21.0 + - - +
97C LEU* 3.2 7.3 + - + +
99C THR* 1.3 76.2 - - - +
101C ASN* 1.3 69.5 + - - +
103C THR* 3.3 4.1 + - - -
104C MET* 2.9 37.7 + - + +
121C LEU* 4.3 8.5 - - + +
122C CYS* 3.9 31.6 - - - +
125C LEU* 4.2 22.7 - - + -
126C PRO* 3.9 12.6 - - + -
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Residues in contact with ASN 101 (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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68C TRP* 2.4 43.0 + - + +
70C LYS 2.8 23.0 + - - +
73C PHE* 3.4 16.9 - - + -
75C TRP* 3.5 27.5 + - - +
76C SER* 5.0 1.4 + - - -
79C VAL* 5.8 0.5 - - - +
97C LEU* 2.9 31.0 + - - +
98C GLU 3.7 5.4 - - - +
99C THR 3.4 0.2 - - - -
100C ILE* 1.3 76.8 - - - +
102C VAL* 1.3 57.1 + - - +
104C MET 3.5 0.3 + - - -
105C ALA* 2.8 29.3 + - - +
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Residues in contact with VAL 102 (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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68C TRP* 3.4 38.4 - - + +
98C GLU 3.3 11.5 + - - +
99C THR 3.7 7.4 - - - +
100C ILE 3.2 0.8 - - - -
101C ASN* 1.3 75.0 - - - +
103C THR* 1.3 63.9 + - - +
105C ALA* 3.1 12.4 + - - +
107C LYS* 3.2 29.2 + - + +
109C VAL* 3.9 20.2 - - + -
275C PHE* 3.8 23.3 - - + -
277C PHE* 3.8 20.6 - - + -
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Residues in contact with THR 103 (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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99C THR 3.0 17.5 + - - -
100C ILE* 3.3 5.1 + - - -
102C VAL* 1.3 74.3 - - - +
104C MET* 1.3 57.7 + - - +
106C GLY* 2.8 15.4 + - - -
107C LYS 4.0 9.4 - - - +
109C VAL* 3.8 14.8 - - + +
122C CYS 4.4 2.2 + - - +
123C TYR* 6.2 0.7 - - - -
126C PRO* 4.8 10.1 - - + -
215C ARG* 2.6 51.7 + - + -
249C SER* 3.7 11.6 + - - +
250C LEU 5.8 0.4 - - - -
251C ILE* 4.0 25.4 - - + +
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Residues in contact with MET 104 (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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75C TRP* 3.6 58.7 - - + +
79C VAL* 5.0 1.3 - - + -
100C ILE* 2.9 34.9 + - + +
101C ASN 3.7 0.2 - - - +
103C THR* 1.3 73.3 - - - +
105C ALA* 1.3 56.1 + - - +
106C GLY* 3.0 10.5 + - - -
126C PRO* 4.0 24.0 - - + -
129C CYS* 3.3 39.0 - - + +
215C ARG* 3.7 25.3 + - - +
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Residues in contact with ALA 105 (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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68C TRP* 3.8 24.5 - - + -
73C PHE* 5.7 0.2 - - + -
75C TRP* 3.9 14.7 - - + -
101C ASN 2.8 15.4 + - - +
102C VAL 3.1 10.9 + - - +
104C MET* 1.3 74.4 - - - +
106C GLY* 1.3 60.9 + - - +
107C LYS* 3.3 18.1 + - + +
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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