Contacts of the helix formed by residues 76 - 85 (chain P) in PDB entry 3PDM
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 LEU 76 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P VAL* 4.7 4.9 - - + -
70P TRP 3.5 9.9 - - - +
73P ASN* 3.3 9.6 + - + +
75P THR* 1.3 83.1 - - - +
77P ALA* 1.3 70.0 + - - +
79P VAL* 2.6 19.7 + - - +
80P PHE* 3.0 38.4 + - + -
128P ILE* 3.3 29.2 - - + -
131P LEU* 4.1 17.0 - - + -
132P LEU* 4.4 14.8 - - + +
136P THR* 3.1 30.5 - - + +
137P ALA* 3.6 6.3 - - + -
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Residues in contact with ALA 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71P VAL 3.1 10.2 + - - +
72P ARG* 3.8 2.9 - - - -
73P ASN 2.4 45.9 + - - +
76P LEU* 1.3 71.1 - - - +
78P PRO* 1.4 64.2 - - + +
79P VAL 2.7 8.7 + - - -
80P PHE* 4.2 2.2 - - - -
81P GLU* 2.9 52.3 + - - +
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Residues in contact with PRO 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73P ASN 3.1 12.8 - - - +
74P PRO* 4.6 6.7 - - + +
75P THR 4.5 5.2 - - - +
76P LEU 3.1 1.9 - - - -
77P ALA* 1.4 85.8 - - + +
79P VAL* 1.3 59.1 + - + +
81P GLU* 4.7 8.3 - - + +
82P ALA* 3.0 21.3 - - - +
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Residues in contact with VAL 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P THR 3.5 16.4 - - - +
76P LEU 2.6 13.4 + - - +
78P PRO* 1.3 73.3 - - - +
80P PHE* 1.3 67.4 + - - +
82P ALA* 3.5 6.3 - - - -
83P LEU* 3.0 19.8 + - - +
124P GLU* 3.5 19.1 - - - +
127P ASN* 3.9 10.3 - - + +
128P ILE* 3.3 40.6 - - + +
131P LEU* 3.5 25.4 - - + -
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Residues in contact with PHE 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P PHE* 6.0 4.3 - + - -
69P VAL* 4.1 13.2 - - + -
70P TRP 2.8 31.9 - - - -
71P VAL* 3.1 41.1 - - + -
76P LEU* 3.0 43.9 + - + -
77P ALA 3.3 6.1 - - - +
79P VAL* 1.3 77.8 - - - +
81P GLU* 1.3 62.0 + - + +
82P ALA 2.8 11.4 + - - -
83P LEU* 3.1 13.9 + - - +
84P LEU* 3.8 16.2 + - + +
128P ILE* 3.6 25.1 - - + -
132P LEU* 5.6 6.1 - - + -
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Residues in contact with GLU 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P VAL* 4.5 11.5 - - + +
72P ARG* 3.9 37.9 + - - -
77P ALA* 3.0 42.7 - - - +
78P PRO* 4.6 5.4 - - + +
80P PHE* 1.3 80.8 - - + +
82P ALA* 1.3 59.5 + - - +
84P LEU* 4.2 15.9 - - + +
85P ARG* 4.2 25.1 + - - +
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Residues in contact with ALA 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78P PRO 3.0 25.5 + - - +
79P VAL 3.3 3.0 + - - +
80P PHE 2.8 2.8 + - - -
81P GLU* 1.3 79.3 - - - +
83P LEU* 1.3 65.0 + - - +
85P ARG* 3.3 16.6 + - - +
86P ALA* 4.1 3.1 + - - +
124P GLU* 3.1 31.7 - - - +
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Residues in contact with LEU 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P LEU* 4.9 4.5 - - + -
44P LEU* 5.7 6.5 - - + -
48P LEU* 5.4 10.1 - - + -
79P VAL 3.0 12.2 + - - +
80P PHE 3.1 3.8 + - - +
82P ALA* 1.3 76.0 - - - +
84P LEU* 1.3 71.5 + - + +
85P ARG 2.8 2.1 + - - -
86P ALA* 2.8 16.6 + - - +
87P THR* 3.1 30.7 - - + +
120P ALA 4.3 1.3 - - - +
121P ILE* 4.1 13.9 - - + +
124P GLU* 3.3 49.5 + - + +
125P ILE* 3.8 19.5 - - + +
128P ILE* 4.2 10.5 - - + -
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Residues in contact with LEU 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P ARG* 5.0 15.7 - - + +
48P LEU* 4.8 19.3 - - + -
49P ILE* 5.1 15.7 - - + -
80P PHE* 3.8 18.1 + - + +
81P GLU* 4.2 17.0 - - + +
83P LEU* 1.3 84.0 - - + +
85P ARG* 1.3 66.6 + - - +
87P THR* 3.2 15.0 + - - -
88P ASP* 2.6 26.2 - - - +
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Residues in contact with ARG 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P GLU* 4.2 15.5 + - - +
82P ALA 3.3 10.6 + - - +
83P LEU 2.8 5.1 + - - -
84P LEU* 1.3 89.5 - - - +
86P ALA* 1.3 57.1 + - - -
87P THR 3.6 0.4 - - - -
88P ASP* 3.8 18.8 - - - +
89P THR* 4.1 12.5 + - - +
3R A 4.1 10.7 + - - +
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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