Contacts of the helix formed by residues 120 - 137 (chain A) in PDB entry 1PV7
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 ALA 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A PHE 5.9 0.4 - - - +
59A PHE* 5.6 0.2 - - + -
60A GLN* 3.5 28.7 - - + +
63A PHE* 3.3 30.0 - - + -
116A PHE* 3.5 18.0 + - + -
119A ASN* 1.3 74.9 + - - +
121A GLY* 1.3 69.3 + - - +
122A ALA 2.7 3.5 + - - -
123A PRO* 2.8 14.6 - - - +
124A ALA* 2.7 17.7 + - - +
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Residues in contact with GLY 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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19A TYR* 3.0 20.1 + - - -
63A PHE* 3.8 5.9 - - - -
80A ILE* 4.5 8.3 - - - -
116A PHE* 4.0 7.8 + - - -
117A CYS* 4.0 7.2 - - - -
119A ASN 3.4 0.8 - - - +
120A ALA* 1.3 80.0 - - - +
122A ALA* 1.3 52.7 + - - +
124A ALA* 2.6 11.6 - - - +
125A VAL* 2.6 36.6 + - - +
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Residues in contact with ALA 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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19A TYR* 3.2 23.3 + - + -
23A MET* 5.1 9.2 - - + -
118A PHE 4.1 11.0 - - - +
119A ASN 3.6 7.6 + - - +
120A ALA 2.7 4.4 + - - -
121A GLY* 1.3 68.4 - - - +
123A PRO* 1.3 75.2 - - + +
124A ALA 2.7 5.4 + - - -
126A GLU* 2.8 39.9 + - + +
1E YIO 6.1 1.6 - - - -
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Residues in contact with PRO 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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60A GLN* 3.5 24.9 - - + +
119A ASN 2.7 27.6 - - - +
120A ALA* 2.9 13.2 - - - +
122A ALA* 1.3 81.5 - - + +
124A ALA* 1.3 54.2 + - - +
126A GLU* 3.5 16.8 - - + +
127A ALA* 2.8 31.8 + - - +
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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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63A PHE* 3.2 29.4 - - + -
77A LEU* 5.2 1.3 - - + -
80A ILE* 4.0 8.5 - - + -
120A ALA 2.7 4.4 + - - -
121A GLY* 2.6 30.3 - - - +
122A ALA 2.7 0.6 - - - -
123A PRO* 1.3 74.5 - - - +
125A VAL* 1.3 54.0 + - - +
127A ALA* 2.5 28.2 + - - +
128A PHE* 3.0 14.7 + - - +
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Residues in contact with VAL 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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15A PHE* 3.7 22.9 - - + +
16A PHE* 3.8 7.7 - - + -
19A TYR* 4.2 32.1 - - + -
20A PHE* 6.5 0.4 - - + -
77A LEU* 3.5 29.4 - - + +
80A ILE* 4.5 5.2 - - + -
121A GLY 2.6 17.8 + - - +
122A ALA 4.3 0.9 - - - +
124A ALA* 1.3 73.1 - - - +
126A GLU* 1.3 61.6 + - + +
127A ALA 3.3 0.7 + - - -
128A PHE* 4.3 2.2 - - - +
129A ILE* 3.1 50.2 + - + +
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Residues in contact with GLU 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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16A PHE* 4.1 23.6 - - + -
19A TYR* 6.0 2.2 - - + -
20A PHE* 6.0 4.5 - - + -
122A ALA* 2.8 29.7 + - + +
123A PRO* 3.5 23.3 - - + +
125A VAL* 1.3 77.4 - - + +
127A ALA* 1.3 60.2 + - - +
130A GLU* 3.3 25.5 + - - +
140A PHE* 5.2 3.5 - - - -
144A ARG* 4.2 23.3 + - - +
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Residues in contact with ALA 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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67A SER* 5.1 9.9 - - - +
123A PRO 2.8 19.0 + - - +
124A ALA* 2.5 15.0 + - - +
126A GLU* 1.3 69.9 - - - +
128A PHE* 1.3 58.3 + - - +
130A GLU* 2.5 40.3 + - - +
131A LYS* 3.1 10.3 + - - +
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Residues in contact with PHE 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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12A PHE* 3.2 25.1 - + - -
67A SER* 5.6 3.2 + - - +
71A GLY 5.2 3.6 - - - -
72A LEU* 3.7 24.2 - - + -
73A ARG 4.1 8.1 - - - -
74A LYS* 3.7 50.5 - - + -
77A LEU* 4.4 24.5 - - + -
124A ALA 3.0 11.7 + - - +
125A VAL* 4.6 1.8 - - - +
127A ALA* 1.3 73.8 - - - +
129A ILE* 1.3 60.2 + - + +
131A LYS* 2.6 36.2 + - - +
132A VAL* 3.0 33.9 + - + +
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Residues in contact with ILE 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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12A PHE* 3.2 40.4 - - + -
15A PHE* 3.9 15.5 - - + -
16A PHE* 3.2 42.0 - - + -
77A LEU* 5.4 1.8 - - + -
125A VAL* 3.1 35.4 + - + +
127A ALA 3.3 0.6 - - - -
128A PHE* 1.3 77.5 - - + +
130A GLU* 1.3 62.1 + - - +
132A VAL* 3.2 12.4 + - + +
133A SER* 3.0 19.9 + - - -
140A PHE* 5.1 1.7 - - + +
143A ALA* 4.8 10.3 - - + -
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Residues in contact with GLU 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 GLU* 3.3 17.7 + - - +
127A ALA* 2.5 24.6 + - - +
129A ILE* 1.3 74.0 - - - +
131A LYS* 1.3 56.0 + - + +
133A SER* 2.9 23.4 + - - -
134A ARG* 3.5 17.5 + - + +
140A PHE* 3.1 57.1 - - + +
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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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67A SER* 3.9 30.1 + - - -
68A ASP* 4.2 15.8 + - - +
71A GLY* 4.5 17.3 + - - +
72A LEU* 4.6 19.7 - - + +
127A ALA* 3.1 11.8 + - - +
128A PHE* 2.6 18.6 + - - +
130A GLU* 1.3 73.6 - - + +
132A VAL* 1.3 60.6 + - - +
134A ARG* 3.0 24.4 + - - +
135A ARG* 3.4 9.4 + - - +
203A ALA* 3.5 33.9 - - + -
204A ASN 5.4 3.1 - - - -
205A HIS* 5.8 1.5 - - - -
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Residues in contact with VAL 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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8A ASN* 4.5 15.7 - - + +
12A PHE* 3.6 18.6 - - + -
72A LEU* 3.8 13.5 - - + -
128A PHE* 3.0 48.2 + - + +
129A ILE* 3.5 6.1 - - - +
130A GLU 3.2 0.2 - - - -
131A LYS* 1.3 76.7 - - - +
133A SER* 1.3 62.5 + - - +
135A ARG* 3.2 7.9 + - + +
136A SER* 3.2 20.8 + - - -
189A THR* 4.2 26.7 - - + +
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Residues in contact with SER 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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129A ILE* 3.0 10.2 + - - -
130A GLU 2.9 15.2 + - - -
132A VAL* 1.3 77.8 - - - +
134A ARG* 1.3 56.3 + - - +
135A ARG 3.1 0.2 - - - -
136A SER* 4.6 2.0 - - - +
137A ASN* 2.9 30.1 + - - +
138A PHE 2.5 36.5 + - - +
139A GLU* 2.9 9.5 + - - -
140A PHE* 3.7 15.0 - - - -
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Residues in contact with ARG 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 GLU* 3.5 14.2 + - + +
131A LYS* 3.0 18.8 + - - +
133A SER* 1.3 79.1 - - - +
135A ARG* 1.3 60.4 + - - +
137A ASN* 4.5 3.6 + - - +
195A ALA* 5.4 3.5 - - - +
202A GLY* 4.3 10.9 + - - +
203A ALA* 2.8 60.9 + - - +
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Residues in contact with ARG 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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8A ASN* 6.0 0.7 - - - +
72A LEU* 5.0 13.5 - - + -
131A LYS 3.4 7.5 + - - +
132A VAL* 3.2 15.9 + - + +
133A SER 3.1 0.4 - - - -
134A ARG* 1.3 83.2 - - - +
136A SER* 1.3 60.6 + - - +
189A THR* 4.1 22.7 - - + +
191A ALA 2.5 31.6 + - - -
192A PRO* 2.8 19.2 + - - +
193A SER* 2.4 35.0 + - - -
195A ALA* 4.5 21.2 - - + +
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Residues in contact with SER 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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2A TYR* 5.2 2.3 - - - -
6A ASN* 3.7 25.3 + - - +
8A ASN* 4.6 24.5 - - - -
9A PHE* 5.3 1.4 + - - +
132A VAL 3.2 14.5 + - - -
133A SER* 4.5 1.8 - - - -
135A ARG* 1.3 82.5 - - - +
137A ASN* 1.3 67.3 + - - +
138A PHE* 3.9 6.9 + - - +
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Residues in contact with ASN 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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2A TYR* 2.7 45.2 + - + -
133A SER 2.9 10.5 + - - -
134A ARG* 4.5 3.1 - - - +
135A ARG 3.6 1.2 - - - -
136A SER* 1.3 87.8 - - - +
138A PHE* 1.3 65.1 + - - +
139A GLU* 3.6 3.2 + - - +
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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