Contacts of the helix formed by residues 108 - 125 (chain A) in PDB entry 2HXI
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 GLY 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ASP* 2.8 24.5 + - - -
106A SER 3.3 2.6 + - - -
107A GLY* 1.3 74.9 - - - +
109A THR* 1.3 60.4 + - - -
111A SER* 3.1 3.8 + - - -
112A ARG* 2.9 39.1 + - - +
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Residues in contact with THR 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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60A ASP* 3.2 4.5 + - - -
64A LEU* 3.8 20.4 - - + -
108A GLY* 1.3 68.9 - - - -
110A GLY* 1.3 65.4 + - - +
112A ARG* 3.2 21.9 + - - +
113A LEU* 3.0 33.2 + - + +
179B ARG* 4.2 23.2 + - - +
180B PHE* 5.1 2.7 - - + -
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Residues in contact with GLY 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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60A ASP* 2.8 21.7 + - - -
63A LEU* 3.7 8.8 - - - +
64A LEU* 3.6 35.1 - - - +
67A MSE 4.3 1.9 - - - +
109A THR* 1.3 72.1 - - - +
111A SER* 1.3 59.8 + - - -
113A LEU* 3.4 5.7 + - - +
114A MSE 3.1 23.9 + - - +
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASP* 3.0 8.0 + - - -
63A LEU* 3.8 14.5 - - - +
101A TRP* 4.8 1.0 + - - -
105A GLY* 5.2 0.5 - - - -
106A SER* 2.6 34.3 + - - -
107A GLY 4.1 0.7 - - - -
108A GLY 3.1 10.5 + - - -
110A GLY* 1.3 75.7 - - - +
112A ARG* 1.3 57.3 + - - +
114A MSE 3.7 5.4 - - - +
115A MSE 2.8 42.5 + - - +
171B ALA* 3.6 19.1 - - - -
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Residues in contact with ARG 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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107A GLY 4.8 5.3 + - - -
108A GLY* 2.9 22.6 + - - +
109A THR* 3.2 23.7 + - - +
111A SER* 1.3 76.4 - - - +
113A LEU* 1.3 58.5 + - - +
115A MSE 4.0 0.2 - - - +
116A GLU* 2.8 33.6 + - - +
169B ARG* 4.5 6.1 - - - +
171B ALA* 2.6 25.1 + - - +
173B LEU 2.9 28.1 + - - -
174B GLY* 3.7 6.5 + - - -
175B ALA* 3.6 31.0 - - - +
180B PHE* 3.7 27.5 - - + -
183B LEU* 3.8 21.3 - - + +
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Residues in contact with LEU 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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64A LEU* 3.8 25.6 - - + +
67A MSE 3.7 34.2 - - + +
109A THR* 3.0 27.1 + - + +
110A GLY* 3.6 5.2 - - - +
111A SER 3.3 0.2 - - - -
112A ARG* 1.3 77.0 - - - +
114A MSE 1.3 61.3 + - - +
116A GLU* 3.9 2.6 - - + +
117A GLU* 3.2 18.0 + - - +
179B ARG* 3.8 25.6 - - - +
180B PHE* 3.9 16.2 - - + -
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Residues in contact with MSE 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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63A LEU* 3.7 22.4 - - + -
67A MSE 4.0 16.7 - - + +
83A VAL* 4.0 9.8 - - + +
87A LEU* 4.0 32.5 - - + -
101A TRP* 4.2 18.4 - - + +
110A GLY 3.1 16.4 + - - +
111A SER* 3.7 4.7 - - - +
113A LEU* 1.3 75.1 - - - +
115A MSE 1.3 78.4 + - + +
117A GLU* 3.3 4.0 + - - +
118A VAL* 3.0 42.4 + - - +
136A TYR* 3.5 23.3 - - - +
140A VAL* 4.5 10.1 - - + -
193B LEU* 5.9 0.9 - - + -
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Residues in contact with MSE 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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111A SER* 2.8 22.2 + - - +
112A ARG 4.0 2.2 - - - +
114A MSE 1.3 86.2 - - + +
116A GLU* 1.4 66.8 + - - +
119A LEU* 2.8 34.5 + - + +
136A TYR* 3.3 37.5 - - + +
170B VAL* 6.1 4.9 - - + -
171B ALA* 3.9 27.8 - - - -
183B LEU* 3.5 33.4 - - + -
187B ALA* 5.3 1.8 - - + -
190B ILE* 3.8 29.8 - - + -
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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
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112A ARG 2.8 18.4 + - - +
113A LEU* 3.9 4.5 - - - +
114A MSE 3.3 0.2 - - - -
115A MSE 1.4 76.0 - - - +
117A GLU* 1.3 58.4 + - - +
119A LEU* 3.9 2.5 - - - +
120A GLN* 2.9 65.7 + - + +
179B ARG 4.4 4.0 - - - +
180B PHE* 3.2 34.5 - - + -
181B PRO* 3.2 8.2 - - - +
182B ALA* 3.0 15.4 + - - -
183B LEU* 2.9 29.8 + - + +
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Residues in contact with GLU 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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67A MSE 4.0 9.9 - - + -
70A TYR* 2.6 38.1 + - + -
72A PRO* 4.1 4.9 - - - +
79A ARG* 2.8 42.1 + - + +
80A LEU* 6.2 0.2 - - + -
83A VAL* 3.5 27.1 - - + -
113A LEU 3.2 15.0 + - - +
114A MSE 3.3 4.0 + - - +
115A MSE 3.2 0.2 - - - -
116A GLU* 1.3 81.8 - - - +
118A VAL* 1.3 55.9 + - - +
120A GLN* 3.4 3.1 + - - +
121A ALA* 2.9 27.4 + - + +
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Residues in contact with VAL 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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80A LEU* 3.8 26.1 - - + +
83A VAL* 4.0 19.7 - - + -
114A MSE 3.0 33.6 + - - +
115A MSE 4.0 2.5 - - - +
117A GLU* 1.3 74.4 - - - +
119A LEU* 1.3 57.3 + - - +
121A ALA* 3.3 1.2 + - - -
122A LEU* 2.8 33.6 + - + +
136A TYR* 3.5 29.6 - - + -
139A LEU* 3.9 17.0 - - + -
140A VAL* 4.4 4.5 - - + -
143A ILE* 6.0 4.0 - - + -
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Residues in contact with LEU 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 MSE 2.8 26.6 + - + +
116A GLU 3.9 0.2 - - - +
118A VAL* 1.3 76.3 - - - +
120A GLN* 1.3 56.7 + - - +
122A LEU* 3.2 5.5 + - + +
123A ARG* 2.8 34.8 + - - +
132A ILE* 3.8 26.2 - - + +
136A TYR* 3.8 29.4 - - + -
182B ALA* 3.9 17.0 - - + +
183B LEU* 3.9 32.5 - - + -
186B PHE* 4.0 11.2 - - + -
190B ILE* 3.9 24.7 - - + -
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Residues in contact with GLN 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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79A ARG* 3.7 19.9 + - - +
116A GLU* 2.9 49.2 + - + +
117A GLU* 3.7 4.3 - - - +
118A VAL 3.4 0.2 - - - -
119A LEU* 1.3 74.4 - - - +
121A ALA* 1.3 56.6 + - - +
123A ARG* 3.2 19.4 + - - +
124A ALA* 2.9 27.9 + - - +
181B PRO* 3.8 14.8 - - - +
182B ALA* 3.4 14.5 - - + +
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Residues in contact with ALA 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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76A TRP* 3.3 28.4 - - + +
79A ARG* 4.0 21.9 - - + +
80A LEU* 3.7 27.8 - - + -
117A GLU* 2.9 17.6 + - - +
120A GLN* 1.3 75.6 - - - +
122A LEU* 1.3 62.4 + - - +
124A ALA* 3.1 7.4 + - - -
125A SER 3.1 17.3 + - - -
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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
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76A TRP* 4.8 2.7 - - + -
80A LEU* 4.1 15.3 - - + -
118A VAL* 2.8 32.1 + - + +
119A LEU* 3.7 4.0 - - + +
121A ALA* 1.3 75.0 - - - +
123A ARG* 1.3 63.0 + - - +
125A SER* 2.7 24.1 + - - -
126A GLY 4.0 0.7 + - - -
127A LEU* 4.2 9.1 + - + +
132A ILE* 3.8 30.6 - - + +
135A ARG* 4.2 11.0 - - + +
136A TYR* 3.6 41.1 - - + +
139A LEU* 4.3 6.1 - - + -
212A LEU* 3.7 30.1 - - + -
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Residues in contact with ARG 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 LEU 2.8 24.0 + - - +
120A GLN* 3.4 24.8 - - - +
122A LEU* 1.3 71.2 - - - +
124A ALA* 1.3 62.4 + - - +
126A GLY* 3.1 16.1 + - - -
127A LEU 4.8 1.3 - - - +
129A ASP* 3.2 24.8 + - - -
132A ILE* 3.6 19.2 - - + +
181B PRO* 5.2 1.4 + - - +
182B ALA* 4.5 11.0 - - - +
185B HIS* 3.8 37.3 + - - +
186B PHE* 3.9 12.7 - - + -
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Residues in contact with ALA 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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76A TRP* 3.8 21.6 - - + +
79A ARG* 4.3 12.8 - - - +
120A GLN 2.9 13.8 + - - +
121A ALA* 3.1 11.6 + - - +
123A ARG* 1.3 77.7 - - - +
125A SER* 1.3 58.7 + - - +
126A GLY* 3.1 1.9 + - - -
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Residues in contact with SER 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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76A TRP* 3.4 51.5 + - - +
121A ALA 3.1 6.0 + - - -
122A LEU* 2.7 21.0 + - - -
124A ALA* 1.3 75.8 - - - +
126A GLY* 1.3 54.9 + - - +
127A LEU* 3.2 26.6 + - - +
213A GLU* 5.7 0.2 - - - +
216A ALA* 3.3 20.6 - - - +
217A PRO 5.0 2.1 - - - +
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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