Contacts of the strand formed by residues 125 - 136 (chain A) in PDB entry 1PNG
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 ARG 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A VAL 3.8 0.5 - - - +
16A LYS* 3.4 5.2 - - - +
17A ASN 2.8 32.4 + - - +
49A ASN* 2.7 39.1 + - - +
56A CYS* 3.5 19.9 - - - -
57A ASP* 2.7 33.1 + - + +
58A GLU* 3.9 5.9 - - - +
59A TRP 3.2 8.5 + - - -
61A ARG* 5.8 1.5 - - + +
83A THR* 3.8 14.7 + - + -
84A PRO* 2.8 32.1 + - - +
86A TRP 4.2 1.6 - - - +
87A VAL 2.8 21.8 + - - -
117A THR* 4.2 15.7 - - + +
119A THR* 5.3 0.2 - - - -
123A LYS 5.0 0.2 - - - -
124A GLY* 1.3 79.0 - - - -
126A GLU* 1.3 59.7 + - - +
127A TYR* 3.3 31.9 - - + +
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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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14A LYS* 3.7 35.2 - - - +
15A VAL 3.1 11.7 - - - +
16A LYS* 4.3 15.6 - - + +
49A ASN* 2.8 26.9 + - - +
50A GLU* 3.2 45.9 + - - +
56A CYS* 5.6 0.6 - - - +
125A ARG* 1.3 73.4 - - - +
127A TYR* 1.3 65.1 + - - +
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Residues in contact with TYR 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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12A PHE 4.0 1.0 - - - +
13A ASP 3.8 0.3 - - - -
14A LYS 2.9 4.9 + - - -
15A VAL* 2.8 51.6 + - + +
17A ASN* 3.3 14.1 - - - -
47A ILE* 3.9 19.5 - - + -
48A LYS 3.1 5.4 - - - +
49A ASN* 3.9 25.8 - - + -
50A GLU* 3.8 2.0 - - - -
63A ALA* 4.1 3.3 - - + +
81A PHE* 3.8 22.7 - + - -
83A THR* 3.5 17.7 - - + +
115A ILE* 3.8 23.8 - - + -
117A THR* 2.7 28.8 + - - +
125A ARG* 3.3 30.6 - - + +
126A GLU* 1.3 79.5 - - - +
128A SER* 1.3 63.1 + - - +
129A VAL* 4.3 3.4 - - + -
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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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12A PHE 2.9 9.2 - - - -
13A ASP* 3.8 6.8 + - - -
14A LYS* 3.0 23.6 + - - +
46A PHE 3.8 0.9 - - - +
47A ILE* 3.7 1.4 - - - -
48A LYS* 2.8 45.7 + - - +
50A GLU* 2.8 23.3 + - - -
127A TYR* 1.3 70.4 - - - +
129A VAL* 1.3 62.2 + - - +
130A ASP* 4.3 2.2 + - - +
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Residues in contact with VAL 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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10A LYS* 4.1 0.3 - - - -
11A THR* 2.7 42.6 + - - +
12A PHE* 2.9 34.3 + - + +
45A MET* 3.3 34.1 - - + -
46A PHE 3.4 11.2 - - - +
47A ILE* 4.5 11.7 - - + -
65A VAL* 5.5 0.2 - - + -
113A LEU* 5.7 0.4 - - + -
115A ILE* 4.3 20.9 - - + -
127A TYR* 4.6 0.7 - - + -
128A SER* 1.3 80.9 - - - +
130A ASP* 1.3 63.7 + - - +
131A PHE* 3.8 7.4 - - + -
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Residues in contact with ASP 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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8A ASN* 2.7 30.3 + - - +
9A ILE 3.2 13.0 - - - +
10A LYS* 4.0 14.1 - - + -
45A MET* 3.8 1.4 - - - -
46A PHE* 2.9 45.5 + - - +
48A LYS* 4.6 15.0 + - - +
94A ARG* 2.9 19.5 + - - -
128A SER 5.0 2.3 - - - +
129A VAL* 1.3 76.4 - - - +
131A PHE* 1.3 65.1 + - - +
132A ASP* 4.3 0.2 - - - +
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Residues in contact with PHE 131 (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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7A VAL 3.6 1.6 - - - +
8A ASN* 3.2 5.0 - - - -
9A ILE* 2.8 41.9 + - + +
11A THR* 3.3 35.0 - - + -
33A PHE* 3.6 33.4 - + + -
43A ILE* 3.9 24.0 - - + -
44A LYS 3.2 4.7 - - - +
45A MET* 3.6 46.7 - - + -
78A ILE* 4.5 7.9 - - + -
100A VAL* 4.2 8.3 - - + -
107A LEU* 4.5 5.4 - - + -
113A LEU* 3.9 17.0 - - + -
129A VAL* 3.8 6.5 - - + -
130A ASP* 1.3 76.3 - - - +
132A ASP* 1.3 64.0 + - - +
133A ILE* 3.8 1.7 + - + -
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Residues in contact with ASP 132 (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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6A THR* 4.5 16.8 - - + +
7A VAL 3.5 3.6 - - - -
8A ASN* 2.8 27.2 - - - +
42A THR 3.6 2.1 - - - +
43A ILE* 3.3 4.0 - - - -
44A LYS* 2.9 35.9 + - + +
46A PHE* 3.6 15.8 - - + -
94A ARG* 2.8 34.1 + - - -
131A PHE* 1.3 71.1 - - - +
133A ILE* 1.3 63.7 + - - +
134A VAL* 3.9 5.8 + - + +
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Residues in contact with ILE 133 (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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5A ASN 3.6 1.4 - - - +
6A THR* 3.2 4.0 - - - -
7A VAL* 2.7 42.3 + - + +
9A ILE* 4.0 11.4 - - + -
33A PHE* 4.0 18.6 - - + -
34A PRO* 4.0 27.1 - - + -
37A VAL* 6.6 0.4 - - + -
40A VAL* 3.6 37.5 - - + -
42A THR 3.6 2.5 - - - +
43A ILE* 4.3 20.2 - - + +
107A LEU 5.3 2.0 - - - +
131A PHE* 4.6 3.1 - - + +
132A ASP* 1.3 76.8 - - - +
134A VAL* 1.3 61.5 + - - +
135A TYR* 3.8 21.9 + - + +
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Residues in contact with VAL 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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5A ASN 3.3 8.7 - - - +
6A THR* 4.0 20.0 - - + +
40A VAL* 3.7 1.0 - - - -
41A LYS* 2.7 43.9 + - + +
42A THR* 2.9 31.9 + - + +
44A LYS* 6.0 2.5 - - + -
132A ASP* 4.7 8.3 - - + +
133A ILE* 1.3 74.8 - - - +
135A TYR* 1.3 62.6 + - - +
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Residues in contact with TYR 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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5A ASN* 2.7 67.7 + - + +
7A VAL* 3.5 21.5 - - + +
34A PRO* 3.3 34.7 - - + +
36A ASP 4.1 12.6 - - - -
39A THR* 3.3 26.0 - - - +
40A VAL* 3.5 26.5 - - + -
41A LYS* 4.6 1.5 - - - +
133A ILE* 3.8 20.9 - - + +
134A VAL* 1.3 81.0 - - - +
136A GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 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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39A THR* 2.8 37.9 + - - +
41A LYS* 3.8 15.7 - - - +
134A VAL 4.1 0.6 + - - -
135A TYR* 1.3 76.2 - - - +
137A THR* 1.3 63.7 + - - -
138A PRO* 3.4 1.3 - - - +
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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