Contacts of the helix formed by residues 113 - 131 (chain A) in PDB entry 2HU2
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 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A SER* 5.7 3.3 + - - -
110A PRO 5.2 1.0 + - - -
112A ALA* 1.3 76.3 - - - +
114A VAL* 1.3 60.3 + - - +
115A GLU 3.4 2.2 - - - -
116A GLU* 3.4 9.9 - - - -
117A THR* 2.6 34.8 + - - -
174A VAL* 5.7 0.2 - - - -
307A TRP* 3.2 43.9 - - - +
312A ALA* 4.0 7.4 - - - -
316A MET* 3.8 12.2 - - - +
600A NAD 4.5 7.1 - - - -
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO 3.7 22.2 - - - +
111A ALA* 3.9 15.5 - - + -
112A ALA 3.6 1.8 + - - -
113A SER* 1.3 78.1 - - - +
115A GLU* 1.3 63.3 + - + +
116A GLU* 4.1 0.4 + - - -
117A THR* 3.7 3.3 - - - -
118A ALA* 3.1 25.5 + - - +
173A ARG* 3.7 48.2 - - + +
174A VAL* 4.0 12.7 - - + +
177A ALA* 4.5 9.0 - - + -
600A NAD 5.4 1.1 - - - +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL* 1.3 81.6 - - + +
116A GLU* 1.3 66.4 + - - +
118A ALA* 3.9 4.0 - - - +
119A ASP* 2.9 40.5 + - - +
177A ALA* 5.1 2.9 - - + +
181A ARG* 3.3 32.8 + - - +
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA 3.7 4.7 - - - +
113A SER* 3.4 17.4 - - - +
114A VAL 4.1 0.2 + - - -
115A GLU* 1.3 80.1 + - - +
117A THR* 1.3 57.8 - - - +
119A ASP* 3.3 8.5 + - - +
120A SER* 3.0 30.8 + - - -
306A ALA 3.3 4.7 - - - +
307A TRP 3.4 22.4 - - - +
308A TYR 4.3 2.9 - - - +
309A SER* 2.9 36.5 + - - +
311A GLN* 5.1 3.1 - - - +
312A ALA* 3.5 15.9 + - - +
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Residues in contact with THR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A SER 2.6 24.2 + - - -
114A VAL 3.7 4.0 - - - -
116A GLU* 1.3 73.8 - - - +
118A ALA* 1.3 57.5 + - - +
120A SER* 3.4 2.3 + - - -
121A THR* 2.7 40.9 + - - +
174A VAL* 3.9 21.5 - - + -
253A THR* 4.3 9.0 - - - +
306A ALA* 3.4 19.0 + - + +
307A TRP* 3.7 5.9 - - - -
600A NAD 3.4 41.0 - - + -
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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
----------------------------------------------------------
114A VAL 3.1 17.0 + - - +
115A GLU* 3.9 6.1 - - - +
116A GLU 3.4 0.2 - - - -
117A THR* 1.3 77.1 - - - +
119A ASP* 1.3 57.7 + - - +
121A THR* 3.7 0.5 - - - -
122A LEU* 3.0 35.0 + - - +
174A VAL* 4.2 3.7 - - - +
177A ALA* 3.7 28.5 - - + -
178A VAL* 3.9 23.3 - - + +
181A ARG* 4.3 8.5 - - - +
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Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU* 2.9 29.0 + - - +
116A GLU* 3.6 7.9 + - - +
117A THR 3.2 0.2 - - - -
118A ALA* 1.3 75.1 - - - +
120A SER* 1.3 58.7 + - - +
122A LEU* 3.6 6.0 + - - +
123A CYS* 3.1 25.1 + - - +
181A ARG* 2.8 32.0 + - - -
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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
----------------------------------------------------------
116A GLU 3.0 10.8 + - - -
117A THR 3.8 0.4 - - - -
119A ASP* 1.3 73.6 - - - +
121A THR* 1.3 61.0 + - - +
123A CYS* 3.3 8.9 + - - +
124A HIS* 2.9 38.2 + - - -
305A ALA 4.5 2.3 + - - -
306A ALA* 3.0 44.5 + - - -
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 2.7 24.4 + - - +
118A ALA 3.7 5.4 - - - -
120A SER* 1.3 74.9 - - - +
122A LEU* 1.3 59.4 + - - +
124A HIS* 3.0 9.0 + - - +
125A ILE* 2.9 37.5 + - + +
178A VAL* 4.0 9.2 - - + -
223A THR* 3.6 14.1 - - - +
225A HIS* 3.5 29.6 - - + +
251A VAL* 4.1 8.7 - - + -
253A THR* 2.9 25.4 + - - +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA 3.0 21.6 + - - +
119A ASP* 3.9 7.0 - - - +
120A SER 3.4 0.2 - - - -
121A THR* 1.3 76.0 - - - +
123A CYS* 1.3 57.4 + - - +
125A ILE* 3.7 16.5 - - + +
126A LEU* 3.0 41.0 + - + +
178A VAL* 3.7 33.0 - - + +
181A ARG* 3.8 29.4 - - + -
182A ALA* 4.6 7.4 - - + +
185A PHE* 3.8 34.8 - - + -
187A PHE* 5.5 2.7 - - + -
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Residues in contact with CYS 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 ASP 3.1 16.1 + - - +
120A SER* 3.3 13.5 - - - +
122A LEU* 1.3 76.8 - - - +
124A HIS* 1.3 56.7 + - + +
126A LEU* 3.4 7.2 + - - +
127A ASN* 2.9 53.2 + - - -
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Residues in contact with HIS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER* 2.9 23.6 + - - -
121A THR 3.0 7.6 + - - +
123A CYS* 1.3 74.9 - - + +
125A ILE* 1.3 64.4 + - - +
127A ASN* 3.3 10.9 + - - +
128A LEU* 3.2 26.3 + - - +
251A VAL* 3.9 9.6 - - + -
253A THR* 3.8 24.2 - - + -
277A ALA* 3.6 31.4 - - + +
278A LEU 4.5 6.3 + - - -
279A ASP* 4.3 6.2 - - + +
300A ILE* 4.4 15.0 - - + +
302A THR* 3.2 42.0 + - + +
306A ALA* 5.7 0.2 - - - +
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 2.9 32.4 + - + +
122A LEU* 3.7 30.1 - - + +
124A HIS* 1.3 73.6 - - - +
126A LEU* 1.3 65.9 + - + +
128A LEU* 3.2 7.2 + - - +
129A TYR* 3.1 32.0 + - + -
166A LEU* 4.1 22.4 - - + -
178A VAL* 4.4 7.6 - - + -
187A PHE* 3.7 34.5 - - + -
221A CYS* 4.4 5.8 - - - -
223A THR* 4.9 2.2 - - - +
251A VAL* 3.9 22.9 - - + -
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Residues in contact with LEU 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 LEU* 3.0 30.2 + - + +
123A CYS* 3.8 6.1 - - - +
125A ILE* 1.3 77.3 - - + +
127A ASN* 1.3 58.0 + - - +
129A TYR* 4.4 2.7 - - - +
130A ARG* 2.8 48.6 + - + +
132A THR* 4.7 1.5 + - - -
161A ILE* 3.5 31.4 - - + -
185A PHE* 3.9 36.6 - - + -
187A PHE* 5.6 1.3 - - + -
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Residues in contact with ASN 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 CYS* 2.9 44.2 + - - +
124A HIS* 3.3 14.7 + - - +
126A LEU* 1.3 76.0 - - - +
128A LEU* 1.3 56.4 + - - +
131A ARG* 3.0 28.5 + - - +
132A THR* 3.5 23.3 + - - +
133A THR* 2.8 29.2 + - - +
134A TRP* 4.4 1.7 - - - -
300A ILE* 4.0 22.4 - - + +
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Residues in contact with LEU 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 HIS 3.2 10.0 + - - +
125A ILE* 3.2 9.0 + - - +
127A ASN* 1.3 77.6 - - - +
129A TYR* 1.3 62.3 + - - +
131A ARG* 4.1 11.4 + - - +
134A TRP* 3.6 32.3 - - + -
157A GLY 5.1 1.9 - - - +
221A CYS* 5.3 0.2 - - - -
249A PHE* 3.5 46.2 - - + -
250A LEU 3.9 11.0 - - - +
251A VAL* 3.8 28.9 - - + -
275A GLY* 3.7 5.6 - - - +
276A ALA 3.6 26.7 - - - +
277A ALA* 4.0 7.2 - - + -
300A ILE* 4.2 5.2 - - + -
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Residues in contact with TYR 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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125A ILE* 3.1 31.7 + - + +
126A LEU* 3.2 5.6 + - - +
128A LEU* 1.3 78.8 - - - +
130A ARG* 1.3 65.4 + - + +
157A GLY 4.5 0.2 - - - +
158A ALA* 3.4 7.0 - - - -
159A ALA* 3.0 50.4 + - + +
160A ARG 4.5 1.3 - - - -
161A ILE* 3.9 26.7 - - + -
164A GLU* 2.8 40.4 + - + +
165A THR 4.9 0.2 + - - -
187A PHE* 3.7 25.3 - + - -
220A ASP* 4.0 4.5 - - - +
221A CYS* 3.6 26.9 - - + +
249A PHE* 3.6 30.4 - + - -
2B ARG* 4.2 1.1 + - - -
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Residues in contact with ARG 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 LEU* 2.8 34.2 + - + +
129A TYR* 1.3 95.2 + - + +
131A ARG* 1.3 73.5 + - - +
132A THR* 3.2 14.0 + - - +
135A LEU* 3.6 11.6 - - - +
158A ALA* 3.6 22.2 - - - +
159A ALA 3.5 19.7 + - - +
161A ILE* 4.4 12.3 - - - -
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Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN 3.0 16.7 + - - -
128A LEU 4.1 10.8 + - - +
130A ARG* 1.3 79.4 - - - +
132A THR* 1.3 53.9 + - - +
133A THR 3.3 2.9 - - - -
134A TRP* 3.2 42.7 + - + +
135A LEU* 2.8 46.7 + - + +
154A VAL 4.1 13.1 + - - -
155A ALA* 4.1 9.0 - - - +
156A SER* 2.8 33.2 + - - +
157A GLY* 4.2 4.8 - - - -
158A ALA* 3.9 22.2 - - + +
274A ARG* 5.3 4.4 + - - +
298A ASN* 3.2 30.7 - - - +
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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