Contacts of the helix formed by residues 93 - 107 (chain A) in PDB entry 4D10
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 GLY 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A SER* 1.3 70.3 - - - +
94A LEU* 1.3 60.5 + - - -
95A MET 3.1 2.2 - - - -
96A ARG 3.0 2.6 + - - -
97A ILE* 3.0 25.0 + - - +
121A PHE* 3.2 34.4 - - - -
125A THR* 6.0 1.8 - - - -
247A TYR* 5.2 1.3 - - - -
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Residues in contact with LEU 94 (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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93A GLY* 1.3 68.5 - - - -
95A MET* 1.3 56.3 + - - +
97A ILE* 3.7 26.6 - - + +
98A GLU* 2.8 48.8 + - + +
127A ASN* 5.4 5.6 - - - +
130A MET* 4.9 14.1 - - + -
209A LEU* 4.1 33.7 - - + +
212A GLY* 5.7 5.8 - - - -
214A LEU* 4.7 19.3 - - + -
247A TYR* 3.6 35.2 + - + -
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Residues in contact with MET 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 3.7 26.5 - - + -
92A SER 3.5 12.5 + - - +
93A GLY 3.1 0.2 - - - -
94A LEU* 1.3 76.8 - - - +
96A ARG* 1.3 57.5 + - - +
98A GLU* 4.0 3.2 - - - +
99A ARG* 3.0 46.5 + - - +
246A VAL* 3.9 14.1 - - + -
247A TYR* 3.4 20.5 + - + +
291A LEU* 5.5 0.4 - - + -
317A PRO 3.7 8.5 - - - +
318A GLU 3.4 20.2 - - - +
319A LEU* 3.4 20.9 - - + +
392A MET* 4.7 2.7 - - - +
393A TYR* 3.7 37.2 - - + +
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Residues in contact with ARG 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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88A ALA* 3.3 25.6 + - - +
89A ALA* 4.7 6.4 + - - +
91A TYR* 2.8 33.9 + - + +
92A SER* 3.5 29.7 + - - +
93A GLY 3.0 9.8 + - - +
95A MET* 1.3 77.1 - - - +
97A ILE* 1.3 57.2 + - - +
99A ARG* 4.0 2.7 - - - +
100A LEU* 3.0 51.0 + - + +
121A PHE* 3.2 49.1 - - + +
124A ARG* 5.5 1.4 - - - +
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY* 3.0 20.7 + - - +
94A LEU* 3.7 27.6 - - + +
96A ARG* 1.3 76.6 - - - +
98A GLU* 1.3 59.2 + - + +
100A LEU* 3.8 6.6 - - - +
101A GLN* 3.0 34.8 + - - +
118A ALA* 5.4 7.1 - - + +
121A PHE* 3.6 26.7 - - + -
122A VAL* 4.3 27.4 - - + -
125A THR* 5.2 7.0 - - - +
127A ASN* 5.5 6.5 - - + +
130A MET* 4.3 27.8 - - + -
134A ILE* 6.1 2.9 - - + -
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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
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94A LEU* 2.8 31.5 + - + +
95A MET* 4.3 2.3 - - - +
97A ILE* 1.3 76.4 - - + +
99A ARG* 1.3 56.7 + - - +
101A GLN* 3.5 13.7 + - - +
102A PHE* 2.9 28.2 + - - +
130A MET* 6.5 0.4 - - - -
214A LEU* 6.0 2.0 - - - +
247A TYR* 3.4 41.4 - - - +
249A GLN* 5.5 4.2 + - - -
392A MET* 3.8 32.3 - - + +
393A TYR* 4.8 1.9 + - - -
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Residues in contact with ARG 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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87A TYR* 4.4 17.6 + - - -
91A TYR* 3.5 55.0 + - - -
95A MET* 3.0 27.9 + - - +
96A ARG* 4.0 3.6 - - - +
98A GLU* 1.3 74.1 - - - +
100A LEU* 1.3 60.7 + - + +
102A PHE* 3.2 7.7 + - - +
103A ILE* 3.0 41.6 + - + +
320A LEU* 4.2 5.3 - - - +
324A ASN* 3.7 10.9 + - - +
328A TYR* 4.0 8.5 + - - -
391A ASP* 3.2 39.2 + - - +
392A MET* 3.9 27.3 - - + +
393A TYR* 4.7 4.2 - - - -
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Residues in contact with LEU 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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84A LEU* 5.1 4.9 - - + +
88A ALA* 4.7 13.2 - - + -
96A ARG* 3.0 42.2 + - + +
97A ILE* 3.8 4.7 - - - +
99A ARG* 1.3 75.2 - - + +
101A GLN* 1.3 58.1 + - - +
103A ILE* 3.5 12.8 + - + +
104A ALA* 2.9 29.0 + - - +
114A ALA* 3.7 41.3 - - + +
117A MET* 3.9 25.4 - - + +
118A ALA* 3.9 26.9 - - + +
121A PHE* 5.4 2.5 - - + -
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Residues in contact with GLN 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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97A ILE* 3.0 24.7 + - + +
98A GLU* 3.7 12.7 - - - +
100A LEU* 1.3 74.5 - - - +
102A PHE* 1.3 56.2 + - - +
104A ALA* 3.6 6.4 - - + +
105A ASP* 2.8 50.3 + - - +
118A ALA* 5.4 0.6 - - - +
130A MET* 4.8 16.8 - - - -
133A GLU* 4.4 16.0 - - - +
134A ILE* 4.6 20.0 - - + +
137A LYS* 3.4 23.3 + - + +
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Residues in contact with PHE 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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98A GLU 2.9 17.4 + - - +
99A ARG* 3.2 10.3 + - - +
101A GLN* 1.3 74.5 - - - +
103A ILE* 1.3 60.4 + - - +
105A ASP* 4.7 2.0 - - - -
106A HIS* 3.0 76.6 + + + +
389A LEU 4.3 1.3 - - - -
390A LEU 3.4 23.3 - - - +
391A ASP 3.2 19.1 - - - -
392A MET* 3.5 42.0 - - + +
395A ALA* 4.2 13.2 - - + -
396A PRO* 5.1 2.5 - - + -
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Residues in contact with ILE 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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82A LEU* 3.9 33.2 - - + -
84A LEU* 3.9 20.4 - - + -
87A TYR* 5.4 16.4 - - + -
99A ARG* 3.0 31.1 + - + +
100A LEU* 3.8 13.0 - - + +
102A PHE* 1.3 76.1 - - - +
104A ALA* 1.3 58.3 + - - +
106A HIS* 5.3 0.4 - - - -
107A CYS* 3.0 42.0 + - + +
110A LEU* 5.0 5.8 - - + +
114A ALA* 4.4 5.8 - - + -
390A LEU* 3.9 22.9 - - + +
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Residues in contact with ALA 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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100A LEU 2.9 17.7 + - - +
101A GLN* 3.6 9.9 - - + +
102A PHE 3.3 0.2 - - - -
103A ILE* 1.3 80.5 - - - +
105A ASP* 1.3 61.0 + - - +
107A CYS 3.7 3.7 - - - +
111A ARG* 2.8 48.3 + - + +
114A ALA* 4.0 16.8 - - + +
115A LEU* 4.6 13.5 - - + +
134A ILE* 6.2 1.3 - - + -
137A LYS* 5.9 3.8 - - + -
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Residues in contact with ASP 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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101A GLN* 2.8 34.4 + - - +
102A PHE* 4.6 1.7 - - - -
104A ALA* 1.3 74.6 - - - +
106A HIS* 1.3 75.1 + - + +
111A ARG* 3.8 13.9 + - - +
137A LYS* 2.8 37.5 + - - +
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Residues in contact with HIS 106 (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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77A VAL* 3.4 30.8 - - + +
102A PHE* 3.0 70.9 + + + +
103A ILE* 5.3 0.4 - - - -
105A ASP* 1.3 87.6 - - + +
107A CYS* 1.3 61.2 + - + +
108A PRO* 3.8 4.2 - - - +
389A LEU 5.2 8.1 - - - +
390A LEU* 5.5 4.0 - - + -
395A ALA* 6.1 0.9 - - + -
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Residues in contact with CYS 107 (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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77A VAL 3.6 15.0 - - - -
78A GLU* 4.5 9.0 - - - -
79A ASN 4.5 2.5 - - - -
103A ILE* 3.0 29.9 + - + +
104A ALA 3.7 8.3 - - - +
106A HIS* 1.3 77.9 - - - +
108A PRO* 1.4 76.6 - - - +
109A THR* 4.9 0.4 - - - -
110A LEU* 3.9 25.0 - - + -
111A ARG* 3.6 13.1 + - - -
390A LEU* 3.7 27.4 - - + -
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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