Contacts of the helix formed by residues 120 - 131 (chain A) in PDB entry 3WH2
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 SER 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLN* 3.8 9.9 + - - -
118A ILE* 3.6 4.3 - - - +
119A ASN* 1.3 81.4 - - - +
121A GLN* 1.3 64.6 + - - +
122A GLU* 3.2 25.0 - - - +
123A GLU* 3.0 25.0 + - - +
124A GLN* 3.2 16.8 + - - +
162A LEU* 3.5 15.8 - - - +
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Residues in contact with GLN 121 (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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120A SER* 1.3 72.8 - - - +
122A GLU* 1.3 70.5 + - - +
124A GLN* 3.3 8.4 + - - +
125A GLU* 3.0 36.7 + - - +
161A SER* 2.9 31.7 + - - -
162A LEU* 3.5 18.3 - - - +
164A PHE* 3.4 13.0 - - - -
189A ARG* 2.9 31.4 + - - +
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Residues in contact with GLU 122 (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 PHE* 3.6 15.4 - - + -
88A GLN* 3.2 23.6 - - - +
120A SER* 3.2 23.6 + - - +
121A GLN* 1.3 87.4 + - - +
123A GLU* 1.3 55.7 + - - +
125A GLU* 3.2 17.8 + - - +
126A PHE* 2.9 29.5 + - - +
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Residues in contact with GLU 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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87A PHE* 3.6 12.8 - - + -
88A GLN* 4.5 6.2 + - - +
92A TYR* 2.6 36.1 + - + +
116A VAL* 4.0 1.8 - - - +
117A VAL 3.2 8.7 - - - +
118A ILE* 4.1 2.9 - - + -
119A ASN* 2.8 29.5 + - - +
120A SER* 3.0 21.7 + - - +
122A GLU* 1.3 74.5 - - - +
124A GLN* 1.3 65.7 + - - +
126A PHE* 3.3 1.2 + - - +
127A LEU* 3.0 41.1 + - + +
206A GLU* 3.1 2.6 - - - +
302A CA 2.5 26.7 - - - -
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Residues in contact with GLN 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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118A ILE* 3.4 21.2 - - + +
120A SER 3.2 4.9 + - - +
121A GLN 3.5 8.7 - - - +
123A GLU* 1.3 76.6 - - - +
125A GLU* 1.3 64.1 + - + +
127A LEU* 3.5 4.1 + - - +
128A SER* 2.8 36.4 + - - -
164A PHE* 3.4 48.3 - - + +
182A MET* 3.4 3.9 - - - +
188A PRO 2.9 23.0 + - - +
191A ASN* 2.9 28.7 + - - -
192A TRP* 3.0 19.1 + - - -
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Residues in contact with GLU 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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121A GLN* 3.0 32.7 + - - +
122A GLU* 3.5 16.3 - - - +
123A GLU 3.2 0.2 - - - -
124A GLN* 1.3 77.2 - - + +
126A PHE* 1.3 65.8 + - - +
128A SER* 3.3 6.1 + - - -
129A TYR* 3.0 25.2 + - - +
188A PRO* 5.6 9.6 - - + +
189A ARG* 5.3 4.0 + - - -
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Residues in contact with PHE 126 (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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85A GLU* 4.0 17.0 - - + -
86A TYR 3.6 13.5 - - - -
87A PHE* 3.5 53.8 - + + -
92A TYR* 4.0 19.5 - + + -
94A PHE* 5.2 0.7 - + - -
122A GLU 2.9 17.0 + - - +
123A GLU 3.7 3.6 - - - +
125A GLU* 1.3 74.9 - - - +
127A LEU* 1.3 70.8 + - + +
129A TYR* 3.2 8.4 + + + +
130A LYS* 2.9 67.7 + - + +
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Residues in contact with LEU 127 (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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92A TYR* 3.7 28.9 - - + -
94A PHE* 4.1 21.8 - - + -
116A VAL* 3.7 25.1 - - + -
118A ILE* 3.8 27.1 - - + -
123A GLU* 3.0 28.7 + - + +
124A GLN 3.9 3.4 - - - +
126A PHE* 1.3 81.5 - - + +
128A SER* 1.3 58.5 + - - +
131A LYS* 2.9 34.3 + - - +
182A MET* 3.9 14.8 - - + -
204A ILE* 4.1 14.4 - - + -
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Residues in contact with SER 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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124A GLN* 2.8 30.3 + - - -
125A GLU 3.7 4.0 - - - -
126A PHE 3.3 0.2 - - - -
127A LEU* 1.3 77.5 - - - +
129A TYR* 1.3 62.0 + - - +
131A LYS* 3.8 13.6 + - - +
182A MET* 3.7 10.0 - - - +
188A PRO* 3.8 21.7 + - - -
191A ASN* 2.8 28.5 + - - +
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Residues in contact with TYR 129 (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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125A GLU 3.0 17.3 + - - +
126A PHE* 3.6 7.9 - + - +
128A SER* 1.3 80.3 - - - +
130A LYS* 1.3 83.4 + - + +
131A LYS 4.5 2.4 - - - +
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Residues in contact with LYS 130 (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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85A GLU* 3.2 35.3 + - - +
94A PHE* 3.8 17.3 - - + -
126A PHE* 2.9 49.2 + - + +
129A TYR* 1.3 97.6 - - + +
131A LYS* 1.3 66.7 + - - +
132A PRO* 3.3 8.5 - - - +
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Residues in contact with LYS 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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94A PHE* 3.6 10.5 - - + -
127A LEU 2.9 18.5 + - - +
128A SER* 4.1 10.1 - - - +
129A TYR 3.4 4.2 - - - +
130A LYS* 1.3 76.9 - - - +
132A PRO* 1.3 90.8 + - + +
133A LYS* 3.4 7.4 + - - +
135A ARG 2.7 24.8 + - - -
137A PHE* 3.5 28.7 - - + -
182A MET* 3.7 28.5 - - + +
183A ARG 3.6 21.3 - - - -
184A ASP* 2.8 28.2 + - - +
191A ASN* 6.1 0.2 - - - +
204A ILE* 5.0 0.4 - - + -
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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