Contacts of the helix formed by residues 75 - 91 (chain A) in PDB entry 2PMP
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 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ASP* 3.9 12.1 - - + +
73A GLY 3.5 4.2 + - - -
74A ALA* 1.3 76.0 - - - +
76A SER* 1.3 60.2 + - - +
77A SER* 3.4 17.3 - - - +
78A VAL* 2.9 30.9 + - + +
79A PHE* 4.0 1.6 + - - -
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Residues in contact with SER 76 (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 ASP* 2.7 34.0 + - - -
41A ASP* 3.8 1.6 - - - +
44A LEU* 3.7 32.4 - - - +
45A HIS* 2.8 26.2 + - - -
48A VAL* 5.0 0.6 - - - +
74A ALA 3.7 0.9 + - - -
75A ALA* 1.3 70.0 - - - +
77A SER* 1.3 64.1 + - - +
78A VAL 3.2 0.2 - - - -
79A PHE* 3.1 23.5 + - - +
80A ILE* 3.1 15.4 + - - +
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.1 5.1 - - - +
75A ALA* 3.4 19.5 - - - +
76A SER* 1.3 76.7 - - - +
78A VAL* 1.3 63.7 + - - +
80A ILE* 3.2 8.4 + - - +
81A LYS* 2.9 31.0 + - - +
122A LEU* 3.7 32.3 - - - -
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Residues in contact with VAL 78 (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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71A TRP* 3.9 27.8 - - + -
74A ALA* 3.9 20.6 - - + -
75A ALA* 2.9 22.5 + - + +
77A SER* 1.3 80.4 + - - +
79A PHE* 1.3 58.0 + - + +
81A LYS* 3.6 5.3 + - - +
82A GLU* 3.1 26.9 + - + +
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Residues in contact with PHE 79 (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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38A SER* 5.7 5.2 - - - -
45A HIS* 4.6 7.9 - + + -
48A VAL* 3.8 14.9 - - + +
60A ILE* 4.5 13.9 - - + -
64A PHE* 3.3 63.9 - + + -
71A TRP* 4.1 14.6 - + + -
72A LYS 5.5 1.6 - - - -
74A ALA* 3.8 39.9 - - + -
76A SER* 3.1 27.2 + - - +
78A VAL* 1.3 76.6 - - + +
80A ILE* 1.3 61.2 + - - +
82A GLU 3.6 0.2 + - - -
83A ALA* 3.0 28.8 + - - +
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Residues in contact with ILE 80 (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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44A LEU* 3.7 30.1 - - + +
47A VAL* 3.7 27.6 - - + -
48A VAL* 3.3 22.4 - - + -
51A ILE* 5.1 1.6 - - + -
76A SER 3.1 15.7 + - - +
77A SER* 3.2 10.3 + - - +
79A PHE* 1.3 77.0 - - - +
81A LYS* 1.3 58.6 + - - +
83A ALA* 3.3 3.5 + - - +
84A VAL* 3.0 27.7 + - - +
119A LEU* 4.6 1.8 - - + -
122A LEU* 3.7 37.7 - - + +
123A LEU* 4.0 14.4 - - + -
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Residues in contact with LYS 81 (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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77A SER* 2.9 24.1 + - - +
78A VAL* 4.1 4.9 - - - +
80A ILE* 1.3 75.3 - - - +
82A GLU* 1.3 63.5 + - - +
84A VAL* 3.1 11.1 - - + +
85A ARG* 3.1 23.2 + - - +
121A LYS* 3.8 17.4 + - - +
122A LEU* 3.4 45.2 + - + +
124A GLY* 5.6 0.4 - - - +
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Residues in contact with GLU 82 (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 ILE* 4.8 3.6 - - + +
64A PHE* 3.6 31.9 - - + -
71A TRP* 5.0 11.9 - - + -
78A VAL* 3.1 18.5 + - + +
79A PHE 3.6 0.2 + - - -
81A LYS* 1.3 76.8 - - - +
83A ALA* 1.3 60.3 + - - +
85A ARG* 2.8 46.6 + - - -
86A LEU* 3.1 35.4 + - + +
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Residues in contact with ALA 83 (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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48A VAL* 4.1 11.2 - - + -
51A ILE* 3.7 24.4 - - + +
52A LEU* 3.8 27.5 - - + +
55A LEU* 4.8 0.2 - - - +
64A PHE* 4.7 1.3 - - + -
79A PHE 3.0 19.0 + - - +
80A ILE* 3.7 6.3 - - - +
81A LYS 3.3 0.2 - - - -
82A GLU* 1.3 78.8 - - - +
84A VAL* 1.3 55.8 + - - +
86A LEU* 3.4 5.2 + - - +
87A MET* 3.0 27.4 + - - +
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Residues in contact with VAL 84 (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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51A ILE* 4.5 6.3 - - + -
80A ILE 3.0 19.7 + - - +
81A LYS* 3.1 27.1 - - + +
83A ALA* 1.3 73.3 - - - +
85A ARG* 1.3 59.1 + - + +
87A MET* 3.6 22.6 - - + +
88A ASP* 3.0 28.8 + - - +
94A ILE* 5.1 0.9 - - + -
122A LEU 4.3 8.5 - - - +
123A LEU* 3.6 47.3 - - + +
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Residues in contact with ARG 85 (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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81A LYS 3.1 17.2 + - - +
82A GLU* 2.8 42.5 + - - +
84A VAL* 1.3 78.3 - - + +
86A LEU* 1.3 73.4 + - - +
88A ASP* 3.3 6.6 + - + +
89A GLU* 2.8 60.0 + - + +
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Residues in contact with LEU 86 (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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52A LEU* 4.8 1.3 - - + -
55A LEU* 4.3 2.6 - - - +
57A LEU* 3.9 26.8 - - + +
63A ILE* 3.7 30.1 - - + -
64A PHE* 5.7 0.2 - - + -
82A GLU* 3.1 33.6 + - + +
83A ALA* 3.4 8.7 + - - +
85A ARG* 1.3 96.9 - - - +
87A MET* 1.3 65.1 + - - +
89A GLU* 3.7 24.7 + - - +
90A ALA* 3.2 22.2 + - - +
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Residues in contact with MET 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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51A ILE* 4.2 9.6 - - + -
55A LEU* 3.6 15.9 - - + +
83A ALA 3.0 16.6 + - - +
84A VAL* 3.6 29.8 - - + +
85A ARG 3.2 0.2 - - - -
86A LEU* 1.3 74.9 - - - +
88A ASP* 1.3 66.7 + - + +
90A ALA* 3.1 10.9 + - - +
91A GLY 3.2 0.5 + - - -
92A TYR* 3.1 46.8 + - + +
93A GLU* 3.9 17.0 - - - -
94A ILE* 4.0 15.9 - - + +
123A LEU 5.3 2.7 - - - +
157A LEU* 3.9 34.1 - - + -
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Residues in contact with ASP 88 (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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84A VAL 3.0 18.8 + - - +
85A ARG* 3.3 8.2 + - + +
87A MET* 1.3 78.2 - - + +
89A GLU* 1.3 58.4 + - - +
91A GLY* 2.9 21.1 + - - -
92A TYR 3.7 9.6 + - - +
160A LYS* 2.6 39.2 + - - +
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Residues in contact with GLU 89 (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 ARG* 2.8 42.1 + - + +
86A LEU* 3.7 26.8 - - + +
88A ASP* 1.3 77.5 + - - +
90A ALA* 1.3 62.0 + - + +
91A GLY 3.2 0.4 - - - -
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Residues in contact with ALA 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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55A LEU* 4.1 22.0 - - + -
57A LEU* 6.0 1.8 - - + -
86A LEU 3.2 17.9 + - - +
87A MET 3.1 7.5 + - - +
89A GLU* 1.3 77.6 - - + +
91A GLY* 1.3 59.3 + - - +
92A TYR* 3.6 8.1 - - + -
159A LYS* 3.1 17.8 + - - -
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Residues in contact with GLY 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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88A ASP 2.9 12.2 + - - -
89A GLU 3.2 1.4 - - - -
90A ALA* 1.3 80.2 - - - +
92A TYR* 1.3 61.5 + - - +
159A LYS* 3.4 22.6 - - - +
160A LYS* 2.9 33.3 + - - +
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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