Contacts of the helix formed by residues 95 - 105 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PRO* 3.6 34.8 - - + -
93A ARG 3.4 0.2 + - - -
94A PRO* 1.3 72.5 - - + +
96A GLN* 1.3 61.7 + - - +
98A GLU* 3.0 33.7 + - + +
99A THR* 2.7 31.7 + - - +
111A LEU* 4.3 8.3 - - + -
113A MET* 4.3 7.9 - - + -
277A PHE* 4.1 11.9 - - + -
278A THR 3.1 18.4 - - - +
279A ALA* 3.1 41.7 - - + +
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Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS 4.4 1.6 - - - +
92A PHE* 3.4 20.8 - - + -
93A ARG* 2.6 48.3 + - + +
94A PRO 2.9 8.3 + - - +
95A LEU* 1.3 79.0 - - - +
97A LEU* 1.3 63.1 + - - +
99A THR* 4.0 1.2 - - - -
100A ILE* 3.2 31.6 + - + +
113A MET* 4.7 5.8 - - + -
117A GLY 4.0 2.8 + - - -
118A GLY* 3.0 38.9 + - - +
121A LEU* 3.4 25.5 - - - +
122A CYS* 3.9 13.4 - - - -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TRP 4.3 1.3 - - - +
69A ASN* 3.4 20.6 - - - +
70A LYS* 3.9 16.2 - - - +
71A GLU* 4.0 26.5 - - + +
76A SER* 6.1 0.9 - - - +
79A VAL* 5.3 6.1 - - + -
92A PHE* 4.1 39.9 - - + +
93A ARG 4.2 0.4 + - - +
95A LEU 3.3 0.4 - - - -
96A GLN* 1.3 82.4 - - - +
98A GLU* 1.3 70.0 + - - +
100A ILE* 3.4 3.4 + - + +
101A ASN* 3.1 49.9 + - - +
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO* 3.3 28.6 - - + +
66A ALA* 5.7 0.2 - - - -
68A TRP* 3.7 10.7 - - + +
69A ASN* 3.4 38.1 + - - +
93A ARG 4.9 0.3 - - - +
95A LEU* 3.0 43.8 + - + +
97A LEU* 1.3 81.2 + - - +
99A THR* 1.3 61.2 + - - +
101A ASN* 3.5 3.1 + - - +
102A VAL* 3.2 27.4 + - - +
277A PHE* 3.8 17.5 - - + -
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Residues in contact with THR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU 2.7 24.2 + - - -
96A GLN 4.0 2.9 - - - -
98A GLU* 1.3 73.8 - - - +
100A ILE* 1.3 60.1 + - - +
102A VAL* 3.4 4.1 + - - +
103A THR* 2.8 32.1 + - - -
109A VAL* 3.9 15.5 - - + -
111A LEU* 3.9 21.9 - - + +
122A CYS* 4.0 15.7 - - + -
251A ILE* 3.7 29.4 - - + -
277A PHE* 3.6 19.0 - - - -
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 4.4 13.5 - - + -
92A PHE* 3.8 25.8 - - + -
96A GLN* 3.2 21.7 + - + +
97A LEU* 3.8 3.8 - - + +
99A THR* 1.3 75.7 - - - +
101A ASN* 1.3 63.2 + - - +
103A THR* 3.1 4.9 + - - -
104A MET* 2.7 50.6 + - + +
121A LEU* 4.3 8.5 - - + +
122A CYS* 3.8 34.1 - - - +
125A LEU* 4.2 22.9 - - + -
126A PRO* 4.0 9.9 - - + -
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Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TRP* 2.6 42.5 + - + -
70A LYS 3.1 19.2 + - - +
73A PHE* 3.5 17.4 - - + -
75A TRP* 3.4 27.2 + - - +
76A SER* 4.8 2.1 + - - -
79A VAL* 5.7 1.0 - - - +
97A LEU* 3.1 25.4 + - - +
98A GLU 3.6 7.4 - - - +
100A ILE* 1.3 79.1 - - - +
102A VAL* 1.3 63.4 + - - +
105A ALA* 3.0 24.9 + - - +
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TRP* 3.5 35.7 - - + +
98A GLU 3.2 13.7 + - - +
99A THR 3.7 7.6 - - - +
100A ILE 3.2 1.0 - - - -
101A ASN* 1.3 77.9 - - - +
103A THR* 1.3 63.5 + - - +
105A ALA* 3.2 9.7 + - - +
107A LYS* 3.1 36.2 + - + +
108A GLU 4.0 0.2 - - - +
109A VAL* 3.6 26.2 - - + -
275A PHE* 3.8 18.8 - - + -
277A PHE* 3.7 20.2 - - + -
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Residues in contact with THR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A THR 2.8 22.6 + - - -
100A ILE* 3.6 5.4 - - - -
102A VAL* 1.3 74.9 - - - +
104A MET* 1.3 56.1 + - - +
106A GLY* 2.8 15.6 + - - -
107A LYS 3.9 9.4 - - - +
109A VAL* 3.6 15.2 - - - +
122A CYS 4.3 2.3 + - - +
123A TYR* 5.8 0.7 - - - -
126A PRO* 4.6 9.2 - - + -
215A ARG* 2.5 52.3 + - + +
249A SER* 3.8 9.4 + - - +
250A LEU 5.7 0.4 - - - -
251A ILE* 4.0 25.1 - - + +
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Residues in contact with MET 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TRP* 3.4 59.2 - - + +
79A VAL* 4.9 0.4 - - + -
100A ILE* 2.7 40.0 + - + +
103A THR* 1.3 67.9 - - - +
105A ALA* 1.3 58.0 + - - +
106A GLY* 3.0 9.1 + - - -
126A PRO* 3.7 24.5 - - + -
129A CYS* 3.1 38.8 - - + +
215A ARG* 3.5 26.2 + - - +
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TRP* 4.2 18.2 - - + -
73A PHE* 6.0 0.2 - - + -
75A TRP* 3.6 16.3 - - + -
101A ASN 3.0 18.1 + - - +
102A VAL 3.4 6.5 - - - +
103A THR 3.2 0.4 - - - -
104A MET* 1.3 74.5 - - - +
106A GLY* 1.3 61.7 + - - +
107A LYS* 3.3 17.0 + - + +
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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