Contacts of the helix formed by residues 125 - 142 (chain A) in PDB entry 3HYW
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 THR 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 3.5 22.7 + - - +
45A PHE* 3.7 9.0 - - - -
109A LEU* 4.2 14.4 - - + -
123A ILE 3.9 0.5 - - - +
124A CYS* 1.3 82.2 - - - +
126A ALA* 1.3 59.6 + - - +
127A GLU* 3.6 15.4 + - - +
128A HIS* 2.8 43.2 + - + +
129A ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 5.7 0.2 - - - +
38A TYR* 3.7 19.9 + - - +
45A PHE* 3.4 25.3 - - + -
48A LEU* 3.6 16.1 - - + +
55A PHE* 3.7 27.4 - - + -
125A THR* 1.3 72.9 - - - +
127A GLU* 1.3 59.7 + - - +
129A ALA* 3.3 0.9 + - - -
130A LEU* 3.0 37.7 + - + +
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 3.1 30.6 + - - +
38A TYR* 2.6 34.7 + - - -
55A PHE* 5.4 0.5 - - - -
125A THR* 3.6 8.4 - - - +
126A ALA* 1.3 77.4 + - - +
128A HIS* 1.3 62.3 + - + +
130A LEU* 3.6 9.9 + - + +
131A GLU* 3.4 26.4 + - - +
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Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.9 24.4 - - + +
111A PHE* 4.1 17.9 - + - -
117A GLU* 4.9 8.8 + - + +
122A SER* 3.1 38.4 + - - +
125A THR* 2.8 33.8 + - + +
127A GLU* 1.3 76.6 - - + +
129A ALA* 1.3 65.4 + - - +
131A GLU* 3.2 25.1 + - - +
132A THR* 3.0 18.4 + - - -
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Residues in contact with ALA 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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45A PHE* 3.5 25.6 - - + +
48A LEU* 4.2 8.7 - - + -
49A ALA* 3.3 25.5 - - + +
122A SER 3.5 7.3 + - - -
123A ILE* 4.1 8.5 - - - +
125A THR 2.9 18.1 + - - +
126A ALA* 3.3 5.4 + - - +
128A HIS* 1.3 77.1 - - - +
130A LEU* 1.3 56.6 + - - +
132A THR* 3.3 2.0 + - - -
133A GLN* 3.0 23.0 + - - +
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Residues in contact with LEU 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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48A LEU* 3.9 26.7 - - + -
55A PHE* 4.8 17.7 - - + -
126A ALA* 3.0 26.6 + - + +
127A GLU* 3.8 9.0 - - + +
128A HIS 3.2 0.2 - - - -
129A ALA* 1.3 73.2 - - - +
131A GLU* 1.3 64.2 + - + +
133A GLN* 3.3 26.3 + - - +
134A LYS* 3.2 32.2 + - - +
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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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121A THR* 5.2 2.9 - - + -
127A GLU 3.4 16.6 + - - +
128A HIS* 3.2 25.4 + - - +
130A LEU* 1.3 75.3 - - - +
132A THR* 1.3 62.7 + - - +
134A LYS* 3.2 16.4 + - - +
135A LYS* 3.2 26.7 + - + +
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Residues in contact with THR 132 (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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49A ALA* 4.1 7.2 - - + -
121A THR* 3.2 37.6 - - - +
122A SER 2.9 25.7 + - - -
123A ILE* 4.2 3.4 - - + -
128A HIS 3.0 4.3 + - - -
129A ALA 3.3 10.1 - - - -
131A GLU* 1.3 73.4 - - - +
133A GLN* 1.3 63.5 + - - +
135A LYS* 3.1 3.1 + - - +
136A LEU* 2.9 24.0 + - + +
163A PHE* 3.8 32.8 - - + -
247A PHE* 4.0 5.4 - - + -
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Residues in contact with GLN 133 (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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48A LEU 2.8 21.5 - - - +
49A ALA 3.2 20.8 + - - +
50A MET 4.6 1.8 - - - +
51A GLY* 3.5 23.0 - - - -
53A ARG 4.7 4.0 + - - +
129A ALA 3.0 11.7 + - - +
130A LEU* 3.4 27.2 - - - +
131A GLU 3.3 0.2 - - - -
132A THR* 1.3 74.5 - - - +
134A LYS* 1.3 64.0 + - + +
136A LEU* 3.3 13.0 + - - +
137A GLN* 3.4 21.1 + - + +
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Residues in contact with LYS 134 (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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130A LEU* 3.2 20.6 + - - +
131A GLU* 3.2 13.6 + - + +
132A THR 3.2 0.4 - - - -
133A GLN* 1.3 79.5 - - + +
135A LYS* 1.3 60.4 + - + +
137A GLN* 3.7 18.3 + - - +
138A GLU* 4.0 5.5 + - - +
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Residues in contact with LYS 135 (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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118A GLU 4.8 3.6 + - - -
119A ASN* 3.2 29.5 + - - +
120A SER 3.7 11.1 + - - +
121A THR* 3.4 20.4 - - + +
131A GLU* 3.2 14.1 + - + +
132A THR 3.1 7.9 + - - +
134A LYS* 1.3 76.3 - - + +
136A LEU* 1.3 65.5 + - - +
137A GLN 3.3 0.2 - - - -
138A GLU* 3.3 32.4 + - - +
139A LEU* 3.4 5.0 + - - +
246A LYS 6.0 1.8 - - - -
247A PHE* 4.2 23.8 - - + +
248A THR 5.8 0.2 + - - -
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Residues in contact with LEU 136 (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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49A ALA 3.3 24.7 - - - +
50A MET* 3.8 25.1 - - - -
132A THR* 2.9 13.4 + - + +
133A GLN* 3.3 8.7 + - + +
135A LYS* 1.3 75.8 - - - +
137A GLN* 1.3 65.6 + - - +
139A LEU* 2.9 24.8 + - + +
140A TYR* 3.1 33.1 + - + +
163A PHE* 3.8 10.5 - - + -
167A LEU* 3.6 27.8 - - + -
247A PHE* 3.6 28.9 - - + -
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Residues in contact with GLN 137 (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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133A GLN* 3.4 19.4 + - + +
134A LYS* 3.8 11.9 - - - +
136A LEU* 1.3 76.3 - - - +
138A GLU* 1.3 61.0 + - - +
140A TYR* 3.4 17.5 + - - +
141A ALA* 3.2 22.3 + - - +
174A ARG* 3.6 24.9 + - - +
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Residues in contact with GLU 138 (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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134A LYS 4.0 3.5 + - - +
135A LYS* 3.3 29.9 + - - +
136A LEU 3.1 0.2 - - - -
137A GLN* 1.3 77.3 - - - +
139A LEU* 1.3 58.3 + - - +
141A ALA* 3.6 6.5 + - + +
142A ASN* 3.0 28.3 + - - +
246A LYS* 3.6 20.8 + - - +
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Residues in contact with LEU 139 (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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135A LYS 3.4 6.2 + - - +
136A LEU* 2.9 31.2 + - + +
138A GLU* 1.3 77.2 - - - +
140A TYR* 1.3 66.3 + - + +
142A ASN 3.1 4.7 - - - +
143A PRO* 3.1 30.6 - - + +
144A GLY 3.7 33.4 - - - +
146A VAL* 3.6 27.1 - - + -
167A LEU* 4.3 13.0 - - + -
171A LEU* 4.5 13.0 - - + -
176A ILE* 4.9 0.7 - - - +
180A VAL* 4.6 3.6 - - + -
246A LYS* 4.4 7.2 - - + +
247A PHE* 4.1 20.9 - - + +
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Residues in contact with TYR 140 (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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50A MET* 3.6 19.8 + - - +
136A LEU* 3.1 39.1 + - + +
137A GLN* 3.4 23.1 + - - +
138A GLU 3.4 0.2 - - - -
139A LEU* 1.3 78.9 - - + +
141A ALA* 1.3 62.0 + - - +
143A PRO* 4.0 5.4 - - - +
167A LEU* 3.9 11.2 - - + +
170A GLU* 3.4 25.9 - - + +
171A LEU* 3.7 28.9 - - + -
174A ARG* 3.4 46.2 - - - +
176A ILE* 3.8 23.5 - - + +
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Residues in contact with ALA 141 (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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137A GLN 3.2 14.4 + - - +
138A GLU* 3.8 8.1 - - - +
140A TYR* 1.3 79.8 - - - +
142A ASN* 1.3 74.9 + - - +
143A PRO* 3.6 6.1 - - - +
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Residues in contact with ASN 142 (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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138A GLU* 3.0 13.9 + - - +
139A LEU* 3.1 6.2 - - - +
141A ALA* 1.3 92.5 - - - +
143A PRO* 1.3 67.8 - - - +
144A GLY 3.6 0.3 + - - -
246A LYS* 3.0 39.3 + - - +
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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