Contacts of the helix formed by residues 86 - 103 (chain A) in PDB entry 1PN9
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 ASP 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASP* 5.0 0.8 + - - -
84A PRO* 3.3 1.4 - - - +
85A LYS* 1.3 75.5 - - - +
87A PRO* 1.3 65.6 - - - +
88A GLN* 3.4 12.1 + - - +
89A LYS* 3.0 53.0 + - + +
90A ARG* 2.8 32.7 + - - +
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Residues in contact with PRO 87 (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 LYS 3.0 10.0 - - - +
86A ASP* 1.3 90.3 - - - +
88A GLN* 1.3 56.7 + - - +
90A ARG* 3.7 1.4 - - + +
91A ALA* 2.8 31.7 + - - +
71B TYR* 3.7 13.4 - - + +
74B GLU* 4.3 22.9 - - + +
75B LYS* 4.0 42.2 - - + +
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Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP* 3.3 12.1 + - - +
87A PRO* 1.3 79.0 - - - +
89A LYS* 1.3 65.7 + - + +
91A ALA* 3.1 11.4 + - - +
92A VAL* 3.2 15.5 + - + +
60B PHE* 3.5 50.4 - - + +
71B TYR* 4.0 11.8 - - + -
75B LYS* 4.8 12.8 + - - +
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP* 5.1 4.2 + - - -
84A PRO* 3.4 34.7 - - + +
86A ASP* 3.0 35.8 + - + +
88A GLN* 1.3 75.7 - - + +
90A ARG* 1.3 63.5 + - - +
92A VAL* 3.1 17.6 + - - +
93A VAL* 3.2 15.6 + - - +
148A ALA* 5.1 3.5 - - - +
151A ASP* 5.4 8.7 + - - -
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Residues in contact with ARG 90 (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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74A GLU* 3.5 22.2 + - - +
83A TYR* 3.1 57.9 + - + +
84A PRO* 3.0 25.6 + - - +
85A LYS* 3.6 29.3 + - - +
86A ASP 2.8 18.5 + - - +
87A PRO 3.8 3.4 - - - +
89A LYS* 1.3 73.2 - - - +
91A ALA* 1.3 57.0 + - - +
93A VAL* 3.2 7.5 + - - +
94A ASN* 2.8 40.7 + - - +
70B ILE* 5.2 0.2 - - - -
74B GLU* 3.4 35.7 + - - +
90B ARG* 3.7 6.7 - - - +
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Residues in contact with ALA 91 (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 PRO 2.8 18.9 + - - +
88A GLN 3.1 6.7 + - - +
90A ARG* 1.3 76.0 - - - +
92A VAL* 1.3 59.8 + - - +
94A ASN* 3.4 8.5 + - - +
95A GLN* 2.9 28.8 + - - +
60B PHE* 4.0 4.9 - - + -
62B LEU* 3.6 22.7 - - + +
67B ALA* 4.1 3.7 - - - +
71B TYR* 3.8 25.6 - - + +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 3.5 15.0 - - + +
89A LYS* 3.1 9.7 + - - +
91A ALA* 1.3 73.8 - - - +
93A VAL* 1.3 61.3 + - - +
95A GLN* 3.4 5.6 + - - +
96A ARG* 2.9 52.4 + - - +
144A GLN* 6.1 0.9 - - - +
148A ALA* 3.9 31.6 - - + +
60B PHE* 3.7 24.9 - - + -
62B LEU* 4.8 2.2 - - + -
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU 5.0 0.2 - - - +
83A TYR* 3.8 27.4 - - + -
84A PRO* 4.4 13.9 - - + -
89A LYS 3.2 11.2 + - - +
90A ARG* 3.2 9.3 + - - +
92A VAL* 1.3 78.7 - - - +
94A ASN* 1.3 56.9 + - - +
96A ARG* 3.3 4.2 + - - +
97A LEU* 2.9 32.4 + - + +
148A ALA* 3.5 24.0 - - + -
153A THR* 3.9 23.6 - - + +
154A ILE* 5.0 0.9 - - + +
155A ALA* 3.9 19.5 - - + +
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Residues in contact with ASN 94 (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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70A ILE* 4.0 5.9 - - - +
83A TYR* 2.8 33.3 + - - -
90A ARG* 2.8 30.1 + - - +
91A ALA* 3.8 6.0 - - - +
93A VAL* 1.3 75.4 - - - +
95A GLN* 1.3 65.5 + - - +
97A LEU* 3.2 12.0 + - - +
98A TYR* 2.9 36.2 + - + -
67B ALA* 3.9 15.5 + - + -
70B ILE* 3.7 33.4 - - - +
98B TYR* 5.1 1.2 + - - -
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Residues in contact with GLN 95 (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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91A ALA 2.9 18.9 + - - +
92A VAL* 3.7 5.7 - - - +
93A VAL 3.3 0.2 - - - -
94A ASN* 1.3 76.2 - - - +
96A ARG* 1.3 99.0 + - - +
98A TYR 3.3 0.7 + - - -
99A PHE* 2.8 42.7 + - - +
140A PHE* 4.4 2.8 - - - -
49B GLN* 4.2 3.0 + - - -
62B LEU* 3.9 10.3 - - + -
63B TRP* 3.3 54.7 - - + +
64B GLU* 3.7 12.1 - - + +
67B ALA* 3.6 7.6 - - + +
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Residues in contact with ARG 96 (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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92A VAL* 2.9 31.2 + - - +
93A VAL* 3.5 5.2 - - - +
95A GLN* 1.3 118.2 + - - +
97A LEU* 1.3 56.6 + - - +
99A PHE* 3.3 9.8 + - + +
100A ASP* 2.9 27.4 + - - +
137A LEU* 6.1 0.2 - - + -
140A PHE* 3.2 60.2 + - + +
144A GLN* 4.1 4.8 + - - +
147A ALA* 2.8 46.2 + - + +
148A ALA 4.4 0.9 - - - +
155A ALA* 3.7 15.0 - - + -
159A LEU* 4.4 9.7 - - + +
63B TRP* 4.4 8.3 - - - -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 3.2 23.7 + - + +
69A GLN* 4.1 4.0 - - - +
70A ILE* 4.2 19.3 - - + -
83A TYR* 4.7 1.3 - - + -
93A VAL* 2.9 28.4 + - + +
94A ASN* 3.2 21.1 + - - +
96A ARG* 1.3 77.9 - - - +
98A TYR* 1.3 61.5 + - - +
100A ASP* 3.2 4.3 + - - +
101A MET 3.2 16.6 + - - -
154A ILE* 3.9 16.4 - - + +
155A ALA* 3.6 25.8 - - - -
158A SER* 3.8 20.6 - - - +
98B TYR* 3.2 21.1 - - - +
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Residues in contact with TYR 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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94A ASN* 2.9 36.3 + - + +
97A LEU* 1.3 73.2 - - - +
99A PHE* 1.3 61.4 + - - +
102A GLY* 2.9 28.9 + - - -
64B GLU* 3.6 28.1 - - + +
66B ARG* 3.5 36.0 - - + +
67B ALA* 4.0 18.2 - - + -
70B ILE* 4.5 6.8 - - + +
94B ASN* 4.5 0.9 + - - -
97B LEU* 3.2 32.1 - - - +
98B TYR* 3.3 49.5 - + - -
101B MET* 3.4 24.5 - - + +
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Residues in contact with PHE 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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95A GLN* 2.8 28.7 + - - +
96A ARG* 3.3 11.4 - - + +
97A LEU 3.2 0.2 - - - -
98A TYR* 1.3 77.3 - - - +
100A ASP* 1.3 64.4 + - - +
103A THR* 2.9 45.2 + - + -
104A LEU* 3.0 29.0 + - + -
133A ALA 3.5 22.2 - - - -
136A PHE* 3.9 11.0 - - + -
137A LEU* 4.0 14.8 - - + -
140A PHE* 3.6 31.2 - + - -
159A LEU* 4.1 15.3 - - + -
49B GLN* 3.7 19.3 - - - -
64B GLU* 4.0 8.9 + - - +
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 2.8 11.8 + - - -
96A ARG 2.9 13.8 + - - +
97A LEU* 3.4 10.1 - - - +
98A TYR 3.2 0.4 - - - -
99A PHE* 1.3 80.5 - - - +
101A MET* 1.3 57.7 + - - +
104A LEU* 3.6 15.6 - - - +
105A TYR* 2.8 34.0 + - - +
158A SER* 2.4 43.3 + - - +
159A LEU* 3.7 10.7 - - + +
162A THR* 2.8 29.1 + - - -
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Residues in contact with MET 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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64A GLU* 3.8 2.9 - - - +
66A ARG* 3.4 30.3 - - - +
97A LEU 3.2 7.2 + - - +
99A PHE 3.3 0.2 - - - -
100A ASP* 1.3 81.0 - - - +
102A GLY* 1.3 58.4 + - - +
105A TYR* 4.2 7.0 - - + +
106A GLN* 3.2 33.0 + - - +
301A GTX 3.4 27.8 - - - +
98B TYR* 3.3 34.1 - - + +
101B MET* 3.2 29.4 - - + -
102B GLY* 3.3 33.9 - - - +
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Residues in contact with GLY 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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98A TYR 2.9 16.3 + - - -
101A MET* 1.3 76.2 - - - +
103A THR* 1.3 59.9 + - - +
106A GLN* 3.5 18.7 - - - +
107A ARG* 5.3 1.7 + - - +
64B GLU* 5.8 0.7 - - - -
101B MET* 3.3 21.4 - - - +
106B GLN* 5.0 5.8 - - - +
302B GTX 5.7 1.8 - - - -
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Residues in contact with THR 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 PHE* 2.9 38.2 + - + -
101A MET 3.4 0.6 - - - -
102A GLY* 1.3 81.4 + - - +
104A LEU* 1.3 66.7 + - - +
105A TYR 3.7 0.7 - - - -
107A ARG* 3.0 57.2 + - - +
133A ALA* 4.0 12.3 - - + -
136A PHE* 4.4 2.9 - - + -
49B GLN* 3.2 23.4 + - - +
64B GLU* 4.4 6.8 + - - -
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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