Contacts of the helix formed by residues 99 - 120 (chain A) in PDB entry 1D1U
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 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A TYR* 4.1 11.9 - - + +
74A ILE* 4.2 2.6 - - - +
97A PRO 3.3 19.5 - - - +
98A LEU* 1.3 76.5 - - - +
100A PRO* 1.3 70.0 - - + +
101A VAL* 3.4 11.1 + - + -
110A ARG 3.6 1.6 - - - +
111A PRO* 3.9 3.3 - - - +
112A VAL* 2.7 47.9 + - + +
113A GLN 4.3 0.4 - - - -
114A ASP* 3.7 19.1 - - + +
1B C 3.1 27.4 - - + +
16C G 3.0 43.1 - - + +
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Residues in contact with PRO 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 6.2 1.8 - - + -
66A MET* 3.4 28.0 - - + -
70A ALA* 3.3 35.2 - - + -
74A ILE* 3.9 9.2 - - + -
98A LEU 4.2 1.1 - - - +
99A LEU* 1.3 84.3 - - + +
101A VAL* 1.3 57.9 + - - +
102A LYS* 2.5 39.2 + - - +
109A TYR* 3.4 14.1 - - + -
110A ARG 4.2 0.7 - - - +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 3.4 11.7 + - + +
100A PRO* 1.3 74.1 - - - +
102A LYS* 1.3 75.6 + - - +
109A TYR* 3.8 0.9 - - - -
110A ARG* 3.4 53.2 + - - +
112A VAL* 3.4 40.4 - - + -
1B C 5.6 3.8 - - - +
16C G 4.9 12.6 - - - +
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PRO* 2.5 28.6 + - - +
101A VAL* 1.3 84.8 - - - +
103A LYS* 1.3 71.6 + - - +
104A PRO* 4.8 0.3 - - - +
105A GLY 4.3 10.8 - - - +
107A ASN 4.3 3.8 - - - +
108A ASP 3.7 16.8 - - - +
109A TYR* 3.6 32.1 - - + -
110A ARG* 5.4 3.6 - - - +
1B C 6.1 3.2 - - - -
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LYS* 1.3 89.1 - - - +
104A PRO* 1.3 72.9 - - + +
105A GLY* 2.6 21.7 + - - +
107A ASN* 3.7 26.4 - - - +
108A ASP* 2.8 40.6 + - - +
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Residues in contact with PRO 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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102A LYS 4.8 0.4 - - - +
103A LYS* 1.3 91.8 - - + +
105A GLY* 1.3 57.0 + - - +
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 4.8 1.0 - - - +
102A LYS* 4.3 12.1 - - - +
103A LYS* 2.6 14.3 + - - +
104A PRO* 1.3 75.0 - - - +
106A THR* 1.3 61.3 + - - -
107A ASN 3.7 1.6 - - - -
109A TYR* 4.7 2.4 + - - -
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Residues in contact with THR 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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69A GLU* 2.7 42.4 + - - +
102A LYS* 5.7 0.4 - - - -
105A GLY* 1.3 74.8 - - - -
107A ASN* 1.3 75.7 + - - +
108A ASP 4.2 0.2 + - - -
109A TYR* 3.2 22.8 - - - -
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Residues in contact with ASN 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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102A LYS* 4.3 3.6 - - - +
103A LYS* 3.7 24.8 - - - +
105A GLY* 3.7 1.2 - - - -
106A THR* 1.3 98.3 + - - +
108A ASP* 1.3 90.5 + - - +
109A TYR* 3.9 2.0 - - - -
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Residues in contact with ASP 108 (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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73A GLY* 5.9 1.5 - - - -
77A HIS* 5.7 3.1 - - + +
102A LYS* 3.7 11.8 - - - +
103A LYS* 2.8 50.6 + - - +
106A THR 4.2 0.4 + - - -
107A ASN* 1.3 89.4 - - - +
109A TYR* 1.3 64.9 + - - +
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Residues in contact with TYR 109 (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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67A SER* 5.4 0.3 + - - -
69A GLU* 2.8 34.7 + - + +
70A ALA* 3.6 19.1 + - + +
73A GLY* 3.9 35.4 + - - -
74A ILE* 4.1 4.0 - - + -
77A HIS* 3.7 18.1 + - - -
100A PRO* 3.4 40.2 - - + -
101A VAL 3.8 5.2 - - - -
102A LYS* 3.6 30.8 - - + +
105A GLY 4.7 1.2 + - - -
106A THR* 3.2 31.9 - - - -
107A ASN 4.2 1.6 - - - -
108A ASP* 1.3 81.4 - - - +
110A ARG* 1.3 71.3 + - - +
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Residues in contact with ARG 110 (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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74A ILE* 4.2 4.8 - - - +
77A HIS* 4.7 8.1 - - + +
99A LEU 3.6 8.1 - - - +
100A PRO* 4.2 1.6 - - - +
101A VAL* 3.4 43.3 + - - +
102A LYS* 5.4 3.1 - - - +
109A TYR* 1.3 82.2 - - - +
111A PRO* 1.3 73.6 - - + +
112A VAL* 3.3 23.4 + - + +
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Residues in contact with PRO 111 (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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74A ILE* 3.5 31.2 - - + -
77A HIS* 3.9 23.1 - - + -
78A ILE* 3.8 20.6 - - + -
81A LEU* 5.3 5.4 - - + -
98A LEU* 4.2 15.7 - - + -
99A LEU 4.0 4.0 - - - +
110A ARG* 1.3 83.9 - - + +
112A VAL* 1.3 63.2 + - - +
113A GLN 4.0 1.4 + - - -
185A TRP* 5.7 10.9 - - + -
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.4 1.5 - - - +
99A LEU* 2.7 47.0 + - + +
101A VAL* 3.4 41.5 - - + -
110A ARG* 3.9 22.4 - - + +
111A PRO* 1.3 77.5 - - - +
113A GLN* 1.3 62.5 + - - +
16C G 4.5 26.0 - - + +
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A THR* 2.9 28.0 + - - +
97A PRO 3.5 11.0 - - - +
98A LEU* 4.2 9.9 - - + -
99A LEU* 4.3 0.7 - - - -
111A PRO 4.0 2.4 + - - -
112A VAL* 1.3 74.6 - - - +
114A ASP* 1.3 62.1 + - - +
115A LEU* 3.4 27.6 + - + +
168A PHE 3.0 21.4 + - - +
169A ALA 3.6 0.2 + - - -
170A PHE* 3.4 24.5 - - - +
185A TRP* 2.9 31.2 + - + -
189A PRO* 5.1 0.3 - - - +
190A GLN 5.0 5.8 + - - +
191A GLY* 4.8 3.3 - - - -
16C G 3.2 21.5 - - - +
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Residues in contact with ASP 114 (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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61A ILE* 5.6 0.7 - - - +
64A TYR* 4.2 4.5 + - - -
96A THR* 3.3 22.8 - - - +
97A PRO* 3.0 25.2 + - + +
99A LEU* 3.7 15.8 - - + +
113A GLN* 1.3 69.8 - - - +
115A LEU* 1.3 58.3 + - - +
116A ARG* 2.8 53.2 + - - +
117A GLU 4.8 1.1 + - - -
2B T 4.9 2.6 + - - +
16C G 3.2 29.3 + - - +
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Residues in contact with LEU 115 (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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96A THR* 3.5 23.8 - - - +
113A GLN* 3.4 24.9 + - + +
114A ASP* 1.3 70.3 - - - +
116A ARG* 1.3 58.0 + - - +
117A GLU 3.4 2.7 - - - -
118A VAL* 3.1 16.0 + - + -
119A ASN* 2.8 33.4 + - - +
168A PHE* 3.8 35.0 - - + -
189A PRO* 4.3 4.0 - - + -
190A GLN 3.3 26.7 - - - +
191A GLY 3.7 6.1 - - - +
192A PHE* 3.6 16.4 - - + +
16C G 2.8 16.4 + - - +
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Residues in contact with ARG 116 (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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114A ASP* 2.8 40.6 + - - +
115A LEU* 1.3 78.1 - - - +
117A GLU* 1.3 64.4 + - + +
119A ASN* 3.5 9.0 + - + +
120A LYS* 3.1 37.9 + - + +
2B T 2.8 24.9 + - - +
3B C 2.9 52.0 + - - +
4B G 4.9 4.3 + - - -
14C G 4.8 1.2 - - - +
15C A 4.3 6.7 + - - -
16C G 3.1 38.3 + - - +
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Residues in contact with GLU 117 (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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59A VAL* 4.1 9.3 - - + +
61A ILE* 3.2 35.9 - - + -
96A THR* 4.8 2.9 - - + -
114A ASP* 4.8 2.2 + - - -
115A LEU 3.4 0.4 - - - -
116A ARG* 1.3 78.9 - - + +
118A VAL* 1.3 61.7 + - - +
120A LYS* 2.8 33.5 + - - +
121A ARG* 2.8 59.4 + - - +
3B C 5.3 5.9 + - - +
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Residues in contact with VAL 118 (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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59A VAL* 5.3 1.1 - - + +
94A TRP* 4.0 20.1 - - + -
95A ASN 6.0 0.2 - - - -
96A THR* 3.8 23.5 - - + +
115A LEU* 3.1 17.5 + - + +
117A GLU* 1.3 78.3 - - - +
119A ASN* 1.3 64.8 + - - +
120A LYS 3.2 0.2 - - - -
121A ARG* 2.8 20.8 + - - +
122A VAL* 3.2 17.1 + - + +
167A LEU* 3.5 45.5 - - + +
168A PHE* 4.0 19.7 - - + -
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Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 2.8 28.6 + - - +
116A ARG* 3.9 8.7 - - + +
118A VAL* 1.3 73.6 - - - +
120A LYS* 1.3 60.7 + - + +
121A ARG 3.1 1.0 + - - -
122A VAL* 3.3 8.4 + - - -
191A GLY 3.0 21.8 + - - -
192A PHE* 3.3 17.2 - - - -
193A LYS* 2.9 71.2 + - + +
16C G 3.9 8.9 + - - -
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Residues in contact with LYS 120 (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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53A LYS* 3.0 29.6 + - - +
116A ARG* 3.1 24.7 + - + +
117A GLU* 2.8 41.0 + - - +
118A VAL 3.2 0.4 - - - -
119A ASN* 1.3 77.2 - - + +
121A ARG* 1.3 62.8 + - + +
122A VAL 3.6 0.2 - - - -
3B C 5.6 0.6 + - - -
4B G 4.4 14.1 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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