Contacts of the helix formed by residues 113 - 131 (chain A) in PDB entry 1HYH
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 ALA 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LEU* 4.0 21.8 - - + +
103A GLN* 4.7 1.8 - - - +
112A PHE* 1.4 76.9 - - - +
114A GLU* 1.3 60.1 + - - +
115A LEU 3.1 0.9 + - - -
116A LYS* 3.6 32.0 + - - +
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Residues in contact with GLU 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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98A GLY* 3.1 4.5 - - - -
99A ASN 2.8 44.6 + - - +
102A LEU* 4.0 17.1 - - + +
103A GLN* 2.8 28.1 + - - +
112A PHE 4.5 1.6 - - - +
113A ALA* 1.3 77.4 - - - +
115A LEU* 1.3 62.0 + - - +
116A LYS 3.3 0.4 - - - -
117A PHE* 2.9 16.5 + - + +
118A THR* 2.9 19.0 + - + +
143A ASN* 3.9 13.0 - - - +
330A NAD 2.6 45.4 + - - -
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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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112A PHE* 3.0 43.8 + - + +
114A GLU* 1.3 76.4 - - - +
116A LYS* 1.3 59.8 + - - +
118A THR* 3.8 4.7 - - - -
119A SER* 2.8 42.8 + - - +
144A PRO* 3.8 24.5 - - + +
147A VAL* 4.1 13.7 - - + -
148A ILE* 4.0 16.2 - - + -
321A ARG* 3.9 23.3 - - + +
325A ILE* 4.8 16.2 - - + -
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Residues in contact with LYS 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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102A LEU* 4.0 29.5 - - + +
113A ALA* 3.6 23.3 + - - +
115A LEU* 1.3 78.2 - - - +
117A PHE* 1.3 58.6 + - - +
119A SER* 3.9 4.6 + - - -
120A SER* 2.6 30.1 + - - -
325A ILE* 6.0 1.3 - - - -
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Residues in contact with PHE 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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98A GLY* 3.4 42.6 - - - -
99A ASN* 3.9 24.2 - - + -
102A LEU* 3.6 19.7 - - + -
114A GLU* 2.9 11.2 + - + +
116A LYS* 1.3 79.0 - - + +
118A THR* 1.3 72.1 + - + +
120A SER* 2.9 21.5 + - - -
121A MET* 3.4 41.7 + - + +
330A NAD 3.9 17.3 - + - -
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Residues in contact with THR 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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97A LEU* 3.9 15.5 - - + +
98A GLY* 3.6 31.0 - - - -
114A GLU* 2.9 20.1 + - - +
115A LEU* 3.8 3.3 - - - -
117A PHE* 1.3 81.4 - - + +
119A SER* 1.3 57.2 + - - +
121A MET* 3.0 22.0 + - - +
122A VAL* 3.2 15.2 + - - +
142A SER* 4.2 5.8 - - - -
143A ASN 2.9 28.1 + - - +
148A ILE* 3.5 18.6 - - - +
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Residues in contact with SER 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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115A LEU* 2.8 33.1 + - - -
116A LYS* 3.9 5.7 + - - -
118A THR* 1.3 77.6 + - - +
120A SER* 1.3 62.2 + - - +
121A MET 3.4 0.3 + - - -
122A VAL* 3.7 8.2 + - - +
123A GLN 4.5 0.2 + - - -
148A ILE* 4.0 6.2 - - - +
151A LEU* 4.1 8.7 - - - -
325A ILE* 3.2 38.7 - - - +
328A THR* 5.4 1.1 - - - +
329A LEU* 3.2 26.1 - - - +
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Residues in contact with SER 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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116A LYS 2.6 18.9 + - - -
117A PHE* 2.9 14.2 + - - -
119A SER* 1.3 80.7 + - - +
121A MET* 1.3 68.5 + - - +
123A GLN* 4.6 7.6 + - - +
124A SER* 5.0 2.9 + - - -
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Residues in contact with MET 121 (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 LEU* 3.8 18.2 - - + -
117A PHE* 3.5 56.5 - - + +
118A THR 3.0 7.9 + - - +
120A SER* 1.3 84.9 - - - +
122A VAL* 1.3 65.1 + - - +
123A GLN 3.4 1.1 - - - -
124A SER* 3.3 9.1 + - - -
125A VAL* 3.1 25.8 + - + +
330A NAD 3.3 30.5 - - - +
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 5.9 2.0 - - + -
118A THR 3.4 15.9 - - - +
119A SER* 3.7 10.0 + - - +
120A SER 3.6 0.6 - - - -
121A MET* 1.3 74.1 - - + +
123A GLN* 1.3 59.7 + - - +
125A VAL* 4.6 0.9 - - - -
126A GLY* 2.7 29.1 + - - +
148A ILE* 3.9 28.9 - - + -
151A LEU* 3.8 35.4 - - + +
152A PHE* 3.9 27.6 - - + -
155A VAL* 3.8 9.7 - - + +
329A LEU* 4.5 4.7 - - + -
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Residues in contact with GLN 123 (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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119A SER 4.5 0.6 + - - -
120A SER 4.6 5.6 + - - +
121A MET 3.4 0.8 - - - -
122A VAL* 1.3 75.3 - - - +
124A SER* 1.3 57.5 + - - +
127A THR* 2.7 46.6 + - - +
155A VAL* 3.4 29.0 - - - +
329A LEU* 2.7 61.3 + - + +
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Residues in contact with SER 124 (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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120A SER 5.0 2.3 + - - -
121A MET* 3.3 14.0 + - - -
123A GLN* 1.3 78.3 - - - +
125A VAL* 1.3 72.5 + - - +
127A THR* 3.9 4.6 - - - -
128A ASN* 2.9 37.1 + - - -
330A NAD 5.0 3.5 + - - -
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Residues in contact with VAL 125 (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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27A ILE* 4.0 22.0 - - + -
84A TRP* 3.9 24.6 - - + -
97A LEU* 3.8 13.0 - - + -
121A MET 3.1 17.8 + - - +
124A SER* 1.3 83.3 + - - +
126A GLY* 1.3 63.1 + - - +
128A ASN* 3.8 2.6 - - - +
129A LEU* 3.0 23.8 + - + +
152A PHE* 3.9 26.5 - - + -
330A NAD 3.7 28.9 - - - +
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Residues in contact with GLY 126 (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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122A VAL 2.7 23.0 + - - -
123A GLN 3.8 0.2 - - - -
125A VAL* 1.3 74.8 - - - +
127A THR* 1.3 59.9 + - - +
129A LEU* 3.3 3.7 + - - +
130A LYS* 3.0 24.1 + - - +
152A PHE* 4.0 10.0 - - - -
155A VAL* 4.0 9.4 - - - -
156A THR* 3.6 24.5 - - - +
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Residues in contact with THR 127 (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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123A GLN* 2.7 39.0 + - - +
124A SER* 3.9 5.2 - - - -
125A VAL 3.4 0.2 - - - -
126A GLY* 1.3 75.1 - - - +
128A ASN* 1.3 60.0 + - - +
130A LYS* 3.3 19.7 + - - +
131A GLU* 2.9 51.1 + - + +
155A VAL* 4.0 3.9 - - - +
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Residues in contact with ASN 128 (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 TRP* 3.5 55.6 - - + +
124A SER* 2.9 30.2 + - - +
125A VAL 3.8 0.9 - - - +
127A THR* 1.3 78.1 - - - +
129A LEU* 1.3 56.7 + - - +
131A GLU* 3.4 7.8 + - - +
132A SER* 2.9 30.5 + - - -
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Residues in contact with LEU 129 (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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27A ILE* 4.5 6.3 - - + -
84A TRP* 4.1 7.1 - - + -
87A LEU* 3.5 31.0 - - + -
93A VAL* 4.2 9.9 - - + -
125A VAL 3.0 18.7 + - - +
126A GLY* 3.5 5.6 - - - +
128A ASN* 1.3 76.7 - - - +
130A LYS* 1.3 60.8 + - - +
132A SER* 2.7 22.4 + - - +
134A PHE* 3.7 32.0 + - + +
138A LEU* 3.6 40.6 - - + -
152A PHE* 5.0 6.1 - - + -
156A THR* 4.6 4.7 - - + -
158A PHE* 4.1 12.2 - - + -
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Residues in contact with LYS 130 (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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126A GLY 3.0 14.1 + - - +
127A THR* 3.6 22.5 + - - +
129A LEU* 1.3 75.7 - - - +
131A GLU* 1.3 74.2 + - - +
132A SER 3.2 1.0 + - - -
133A GLY* 3.3 12.8 + - - -
134A PHE 4.6 1.0 + - - +
155A VAL* 3.6 17.7 + - - +
156A THR* 3.4 29.2 - - - +
158A PHE* 3.8 19.0 - - + -
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Residues in contact with GLU 131 (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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127A THR* 2.9 37.3 + - + +
128A ASN* 3.8 7.9 - - - +
130A LYS* 1.3 88.7 + - + +
132A SER* 1.3 60.1 + - - +
133A GLY* 3.3 1.4 + - - -
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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