Contacts of the helix formed by residues 101 - 119 (chain A) in PDB entry 3ZYQ
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 GLU 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A PRO* 3.6 29.0 - - + +
62A LEU* 5.5 0.5 - - - +
99A GLN* 3.0 17.9 + - - +
100A VAL* 1.3 80.3 - - + +
102A VAL* 1.3 74.7 + - - +
103A ASN* 2.9 33.6 + - - +
104A VAL* 2.9 36.1 + - + +
105A ARG* 3.0 23.8 + - - +
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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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100A VAL 3.9 3.0 + - - -
101A GLU* 1.3 82.5 - - - +
103A ASN* 1.3 70.6 + - - +
105A ARG* 3.3 13.2 + - + +
106A ASN* 2.9 49.5 + - - +
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Residues in contact with ASN 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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62A LEU* 3.7 25.3 - - + +
101A GLU* 2.9 26.5 + - - +
102A VAL* 1.3 82.4 - - - +
104A VAL* 1.3 56.5 + - - +
106A ASN* 3.8 15.3 - - - +
107A LYS* 3.1 27.7 + - - +
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Residues in contact with VAL 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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58A PRO* 3.4 37.2 - - + +
61A ALA* 4.1 9.0 - - + -
62A LEU* 4.0 18.6 - - + +
65A LEU* 4.0 16.3 - - + +
95A LEU* 5.2 4.3 - - + -
99A GLN* 3.6 29.6 - - + +
101A GLU* 2.9 22.3 + - - +
103A ASN* 1.3 73.0 - - - +
105A ARG* 1.3 65.1 + - - +
107A LYS* 3.2 4.7 + - - +
108A ILE* 3.0 31.5 + - + +
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Residues in contact with ARG 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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96A LEU* 2.9 41.4 + - + +
97A LYS* 4.8 4.4 + - - +
99A GLN* 3.5 30.8 + - + +
100A VAL 5.0 1.6 - - - -
101A GLU 3.0 20.9 + - - +
102A VAL* 3.5 17.7 - - + +
104A VAL* 1.3 76.9 - - - +
106A ASN* 1.3 65.7 + - - +
108A ILE* 3.2 6.3 + - - +
109A LEU* 3.1 32.3 + - + +
140A HIS* 3.4 32.5 + - - -
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Residues in contact with ASN 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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102A VAL* 2.9 46.7 + - - +
103A ASN* 3.8 15.9 - - - +
104A VAL 3.3 0.2 - - - -
105A ARG* 1.3 75.5 - - - +
107A LYS* 1.3 57.8 + - - +
109A LEU* 3.4 13.4 + - - +
110A TYR* 2.9 28.5 + - - +
141A VAL 5.7 0.7 - - - +
143A PRO* 4.8 5.7 - - + +
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Residues in contact with LYS 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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62A LEU* 3.8 16.2 - - + -
65A LEU* 3.8 27.6 - - + -
66A GLU* 4.0 27.8 + - - +
69A GLU* 2.7 36.3 + - - -
103A ASN 3.1 17.6 + - - +
104A VAL 3.2 5.1 + - - +
106A ASN* 1.3 75.2 - - - +
108A ILE* 1.3 61.2 + - - +
110A TYR* 3.3 22.4 + - + +
111A LEU* 2.9 33.8 + - + +
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Residues in contact with ILE 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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65A LEU* 4.0 19.1 - - + -
92A LEU* 4.3 24.5 - - + +
95A LEU* 3.8 34.8 - - + +
96A LEU* 4.2 27.6 - - + +
99A GLN* 5.2 1.1 - - + -
104A VAL* 3.0 27.2 + - + +
105A ARG* 3.6 5.8 - - - +
107A LYS* 1.3 75.7 - - - +
109A LEU* 1.3 62.9 + - - +
111A LEU* 3.3 8.3 + - - +
112A ILE* 3.0 44.3 + - + +
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Residues in contact with LEU 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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96A LEU* 3.8 26.0 - - + -
105A ARG* 3.1 20.7 + - + +
106A ASN* 3.6 14.6 - - - +
108A ILE* 1.3 76.8 - - - +
110A TYR* 1.3 62.6 + - - +
112A ILE* 3.4 1.3 + - - -
113A GLN* 3.0 19.8 + - - +
135A MET* 4.4 4.0 - - - -
140A HIS* 3.8 28.3 - - + +
141A VAL 3.7 22.9 - - - +
142A PHE* 3.2 44.3 - - + -
143A PRO* 4.3 5.6 - - + -
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Residues in contact with TYR 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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69A GLU* 3.1 35.2 + - + -
73A LYS* 5.9 1.0 - - - -
106A ASN 2.9 17.6 + - - +
107A LYS* 3.4 21.8 - - + +
109A LEU* 1.3 74.7 - - - +
111A LEU* 1.3 75.6 + - + +
113A GLN* 3.5 4.9 + - - +
114A ALA* 2.9 30.2 + - + +
143A PRO* 4.0 26.1 - - + +
144A GLU 5.9 1.1 - - - -
146A LYS* 4.2 13.1 + - - -
149A ASP* 3.4 51.0 + - + +
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Residues in contact with LEU 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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65A LEU* 3.8 41.5 - - + +
68A MET* 5.0 0.9 - - + -
69A GLU* 3.6 33.7 - - + +
92A LEU* 6.3 0.7 - - + -
107A LYS* 2.9 27.3 + - + +
108A ILE* 3.8 4.3 - - - +
110A TYR* 1.3 89.8 - - + +
112A ILE* 1.3 60.7 + - + +
114A ALA* 4.2 2.7 - - + -
115A TRP* 2.8 77.0 + - + +
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Residues in contact with ILE 112 (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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89A MET* 5.1 6.1 - - + -
92A LEU* 4.7 18.8 - - + -
108A ILE* 3.0 36.0 + - + +
109A LEU* 4.0 2.9 - - - +
111A LEU* 1.3 75.9 - - + +
113A GLN* 1.3 58.6 + - - +
115A TRP* 4.8 2.9 - - + -
116A ALA* 3.0 28.9 + - - +
128A VAL* 3.8 13.2 - - + +
131A THR* 4.4 8.1 - - + -
132A TYR* 3.6 40.2 - - + +
135A MET* 3.1 46.0 - - + -
142A PHE* 4.6 1.6 - - + -
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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
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109A LEU 3.0 16.9 + - - +
110A TYR* 3.7 4.8 + - - +
112A ILE* 1.3 78.8 - - - +
114A ALA* 1.3 60.2 + - - +
116A ALA* 3.3 1.4 + - - +
117A HIS* 2.7 40.9 + - + +
132A TYR* 2.7 44.0 + - + +
142A PHE* 3.4 19.2 - - + +
143A PRO* 2.8 36.8 + - - +
144A GLU 4.1 0.2 - - - -
145A PHE* 3.7 29.8 + - + +
149A ASP* 5.1 2.0 + - - -
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Residues in contact with ALA 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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110A TYR* 2.9 26.2 + - + +
111A LEU* 3.2 8.0 + - + +
113A GLN* 1.3 76.0 - - - +
115A TRP* 1.3 65.2 + - + +
117A HIS 3.4 1.7 + - - -
118A ALA* 2.9 24.8 + - - +
145A PHE* 4.3 12.3 - - - -
149A ASP* 3.8 34.8 - - + +
150A ALA* 3.4 11.4 - - - +
152A PHE* 5.5 0.2 - - - -
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Residues in contact with TRP 115 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A MET* 3.9 32.3 - - + -
69A GLU* 4.7 3.2 + - - +
72A VAL* 3.6 35.7 - - + +
83A VAL* 4.2 21.8 - - + -
88A THR* 5.5 0.2 - - + -
89A MET* 4.4 13.9 - - + -
92A LEU* 4.3 22.2 - - + -
111A LEU* 2.8 61.7 + - + +
112A ILE* 4.8 1.6 - - - -
114A ALA* 1.3 77.7 - - + +
116A ALA* 1.3 60.0 + - - +
118A ALA* 4.1 4.7 - - - -
119A PHE* 2.8 50.1 + + + -
128A VAL* 3.7 14.1 - - + -
152A PHE* 4.0 18.7 - + - -
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Residues in contact with ALA 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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112A ILE 3.0 19.1 + - - +
113A GLN 3.7 4.5 - - - +
114A ALA 3.3 0.2 - - - -
115A TRP* 1.3 79.0 - - - +
117A HIS* 1.3 62.4 + - - +
119A PHE* 3.7 2.6 + - - +
120A ARG* 3.6 17.7 + - - +
128A VAL* 3.7 8.5 - - + +
129A GLN* 3.8 39.1 - - + +
132A TYR* 3.9 22.0 - - + -
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Residues in contact with HIS 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A GLN* 2.7 40.2 + - + +
114A ALA 3.7 6.3 - - - +
115A TRP 3.1 0.2 - - - -
116A ALA* 1.3 76.6 - - - +
118A ALA* 1.3 63.8 + - - +
119A PHE 3.2 0.9 + - - -
120A ARG* 2.9 44.0 + - - +
132A TYR* 4.0 21.9 - + - -
145A PHE* 3.7 44.4 - + + -
150A ALA* 4.0 3.6 - - + -
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Residues in contact with ALA 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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114A ALA 2.9 16.2 + - - +
115A TRP* 3.1 4.9 + - - +
117A HIS* 1.3 75.7 - - - +
119A PHE* 1.3 62.9 + - + +
120A ARG* 3.3 9.0 + - - +
121A ASN* 5.0 1.6 + - - +
122A GLU* 5.6 1.4 - - - +
150A ALA* 3.7 21.2 - - - +
152A PHE* 3.3 42.5 - - + -
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Residues in contact with PHE 119 (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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72A VAL* 4.3 6.5 - - + -
80A HIS* 3.6 49.6 - + + -
83A VAL* 4.5 5.4 - - + -
84A ALA* 3.6 26.5 - - + -
115A TRP* 2.8 38.9 + + + +
116A ALA* 4.0 4.7 - - - +
118A ALA* 1.3 77.6 - - - +
120A ARG* 1.3 57.4 + - - +
121A ASN 3.2 3.4 - - - -
122A GLU* 3.0 32.7 + - + +
125A TYR* 3.7 28.6 - + + +
126A LYS* 5.8 0.5 - - - -
128A VAL* 4.0 13.5 - - + -
129A GLN* 5.4 0.8 - - - +
152A PHE* 3.9 19.3 - + - -
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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