Contacts of the helix formed by residues 97 - 112 (chain A) in PDB entry 2PX7
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ALA* 5.9 0.7 - - - -
95A PHE 3.9 2.2 + - - -
96A VAL* 1.3 76.1 - - - +
98A ARG* 1.3 64.5 + - - +
99A GLY* 3.6 5.3 + - - -
100A LEU* 3.1 23.2 + - - +
101A VAL* 3.2 16.2 + - - +
189A GLU* 2.5 33.5 + - - -
191A THR* 5.4 2.7 - - - -
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Residues in contact with ARG 98 (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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1A MET* 3.5 28.2 - - - +
2A GLU* 4.3 15.3 + - - +
38A ALA 5.5 7.2 - - - +
41A ASP* 2.7 34.2 + - - +
96A VAL 4.1 0.2 + - - -
97A SER* 1.3 73.4 - - - +
99A GLY* 1.3 56.5 + - - +
101A VAL* 3.5 8.5 + - + +
102A ALA* 3.0 43.9 + - - +
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Residues in contact with GLY 99 (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 SER* 3.1 7.0 + - - -
98A ARG* 1.3 80.5 - - - +
100A LEU* 1.3 60.8 + - - +
102A ALA* 4.0 4.0 - - - +
103A ARG* 3.0 39.9 + - - +
189A GLU* 4.8 0.9 - - - -
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Residues in contact with LEU 100 (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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96A VAL* 4.4 10.3 - - + -
97A SER* 3.1 22.3 + - - +
99A GLY* 1.3 71.5 - - - +
101A VAL* 1.3 67.5 + - - +
103A ARG* 3.2 14.0 + - - +
104A VAL* 2.9 31.8 + - + +
116A PRO* 3.8 18.8 - - + -
145A GLN* 4.5 1.8 - - - +
146A THR 4.2 11.9 - - - +
147A PRO* 4.4 9.6 - - + -
187A GLU 3.6 23.8 - - - +
188A GLY* 3.9 3.8 - - - -
189A GLU* 3.8 19.3 + - + +
192A ALA* 3.7 29.6 - - + -
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Residues in contact with VAL 101 (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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2A GLU* 3.6 24.9 - - - +
38A ALA 4.1 15.7 - - - +
39A PHE* 3.7 37.5 - - + -
87A LEU* 3.8 14.7 - - + +
96A VAL* 4.6 11.7 - - + +
97A SER 3.2 15.8 + - - +
98A ARG* 3.8 8.5 - - + +
100A LEU* 1.3 75.6 - - - +
102A ALA* 1.3 56.8 + - - +
104A VAL* 3.1 3.8 + - - +
105A LEU* 2.8 30.7 + - - +
147A PRO* 4.5 10.1 - - + -
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Residues in contact with ALA 102 (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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2A GLU* 4.6 5.4 + - - +
98A ARG* 3.0 34.7 + - - +
99A GLY* 4.0 4.5 - - - +
101A VAL* 1.3 75.5 - - - +
103A ARG* 1.3 54.3 + - - +
105A LEU* 3.8 6.9 - - - +
106A GLU* 2.8 37.7 + - - +
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Residues in contact with ARG 103 (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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99A GLY* 3.0 28.9 + - - +
100A LEU* 3.5 12.1 - - - +
102A ALA* 1.3 75.1 - - - +
104A VAL* 1.3 64.7 + - - +
106A GLU* 3.9 6.0 - - - +
107A ALA* 3.2 23.7 + - - +
186A VAL* 4.0 19.1 - - + +
187A GLU* 2.8 70.3 + - - +
188A GLY 3.6 8.7 + - - -
189A GLU* 3.2 28.2 + - - +
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Residues in contact with VAL 104 (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 LEU* 3.6 20.0 - - + -
100A LEU* 2.9 25.9 + - + +
101A VAL 3.7 3.1 - - - +
103A ARG* 1.3 76.5 - - - +
105A LEU* 1.3 59.3 + - - +
107A ALA* 3.3 2.6 + - - +
108A ALA* 2.9 27.4 + - - +
114A ALA* 3.8 10.0 - - - +
116A PRO* 4.0 19.1 - - + -
147A PRO* 3.3 38.4 - - + +
149A GLY 3.6 14.8 - - - +
186A VAL* 4.1 14.4 - - + -
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Residues in contact with LEU 105 (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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2A GLU* 3.6 36.8 - - + +
3A VAL* 4.0 13.9 - - + -
85A LEU* 3.1 31.0 - - + -
86A VAL 6.0 0.2 - - - -
87A LEU* 4.2 30.7 - - + +
101A VAL 2.8 20.0 + - - +
102A ALA* 3.8 5.2 - - - +
104A VAL* 1.3 73.3 - - - +
106A GLU* 1.3 57.0 + - - +
108A ALA* 3.1 4.8 + - - +
109A GLN* 2.8 53.5 + - - +
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Residues in contact with GLU 106 (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 ALA 2.8 22.9 + - - +
103A ARG* 3.9 7.4 - - - +
105A LEU* 1.3 73.8 - - - +
107A ALA* 1.3 63.2 + - - +
109A GLN* 3.4 23.8 + - - +
110A ARG* 2.5 59.1 + - - +
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Residues in contact with ALA 107 (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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103A ARG 3.2 9.6 + - - +
106A GLU* 1.3 77.3 + - - +
108A ALA* 1.3 59.9 + - - +
110A ARG* 3.3 22.3 + - - +
111A SER* 2.8 36.1 + - - +
114A ALA* 3.7 11.9 - - + -
184A ALA* 5.5 4.7 - - + -
186A VAL* 3.6 30.5 - - + -
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Residues in contact with ALA 108 (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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85A LEU* 4.1 11.0 - - + -
87A LEU* 5.3 0.4 - - + -
104A VAL 2.9 17.0 + - - +
105A LEU* 3.1 7.8 + - - +
107A ALA* 1.3 77.9 - - - +
109A GLN* 1.3 57.0 + - - +
111A SER* 4.1 2.9 - - - -
112A GLY* 2.8 29.6 + - - +
113A ALA 4.5 1.3 - - - +
114A ALA* 3.7 6.9 - - + +
149A GLY* 3.6 35.2 - - - +
150A PHE* 3.9 3.8 - - - +
151A PHE* 3.3 6.1 - - - -
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Residues in contact with GLN 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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3A VAL* 5.2 4.2 - - - +
85A LEU* 3.6 24.7 - - + +
105A LEU* 2.8 39.3 + - - +
106A GLU* 3.6 23.9 - - - +
107A ALA 3.3 0.2 - - - -
108A ALA* 1.3 74.9 - - - +
110A ARG* 1.3 61.9 + - + +
151A PHE* 3.5 14.5 - - - -
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Residues in contact with ARG 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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106A GLU* 2.5 51.0 + - - +
107A ALA* 3.3 22.1 + - - +
108A ALA 3.2 0.4 - - - -
109A GLN* 1.3 81.3 - - + +
111A SER* 1.3 67.2 + - - +
112A GLY 3.6 0.6 + - - -
151A PHE* 4.3 5.6 - - - -
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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
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107A ALA* 2.8 21.7 + - - -
110A ARG* 1.3 83.0 - - - +
112A GLY* 1.3 59.3 + - - +
113A ALA 2.9 29.5 + - - +
151A PHE* 4.2 1.8 - - - -
181A TYR* 2.8 25.3 + - - -
182A PRO* 4.8 2.2 - - - +
184A ALA* 4.0 16.2 - - - +
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Residues in contact with GLY 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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108A ALA 2.8 18.2 + - - -
111A SER* 1.3 75.6 - - - +
113A ALA* 1.3 59.7 + - - +
149A GLY 4.3 0.2 - - - -
150A PHE* 3.2 5.6 - - - -
151A PHE* 3.0 52.3 + - - -
154A LEU* 3.3 13.1 - - - +
181A TYR* 3.9 1.8 - - - -
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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