Contacts of the strand formed by residues 64 - 72 (chain A) in PDB entry 1PMN
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 TYR 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A TYR* 2.8 29.1 + - - -
60A VAL* 4.3 7.0 - - + -
61A LEU* 3.1 19.1 + - + +
63A ARG* 1.3 107.0 + - + +
65A GLN* 1.3 60.6 + - - +
67A LEU* 4.0 4.3 - - + +
81A ALA* 4.6 1.1 - - + -
82A TYR 3.4 2.5 - - - +
83A ASP* 3.5 38.0 + - + -
90A VAL* 4.0 11.2 - - + -
92A ILE* 3.8 23.8 - - + -
127A LEU* 5.6 0.7 - - - +
128A ASN* 2.9 35.5 + - - +
130A PHE* 3.8 27.1 - + - -
145A VAL* 3.9 22.0 - - + +
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Residues in contact with GLN 65 (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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49A TYR* 3.7 7.9 - - + +
62A LYS 3.6 16.2 + - - +
63A ARG 4.0 5.4 - - - +
64A TYR* 1.3 79.2 - - - +
66A ASN* 1.3 72.8 + - + +
67A LEU* 3.4 3.9 + - - +
81A ALA* 3.6 1.6 - - - -
82A TYR* 2.8 48.1 + - + +
84A ALA* 4.0 17.5 - - - +
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Residues in contact with ASN 66 (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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49A TYR* 4.3 3.6 + - - -
65A GLN* 1.3 81.4 - - + +
67A LEU* 1.3 71.9 + - - +
68A LYS* 3.6 7.9 + - - +
80A ALA 3.9 4.0 - - - +
81A ALA* 4.4 2.1 - - - -
82A TYR* 5.2 6.1 - - + +
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Residues in contact with LEU 67 (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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49A TYR* 3.6 23.1 + - + +
51A VAL* 4.4 15.5 - - + +
53A VAL* 4.6 8.7 - - + -
58A PHE* 3.6 44.4 - - + -
60A VAL* 4.2 17.0 - - + -
64A TYR* 4.0 12.3 - - + +
65A GLN 4.2 1.1 - - - -
66A ASN* 1.3 83.2 - - - +
68A LYS* 1.3 61.3 + - - +
69A PRO* 4.6 1.9 - - - +
79A CYS* 4.3 13.9 - - + -
80A ALA 3.2 7.4 - - - +
81A ALA* 4.1 18.6 - - + -
92A ILE* 4.6 3.4 - - + -
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Residues in contact with LYS 68 (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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66A ASN* 4.1 7.0 - - - +
67A LEU* 1.3 78.6 - - - +
69A PRO* 1.3 84.7 - - + +
70A ILE* 3.3 16.5 - - - +
79A CYS* 3.2 4.0 - - - +
80A ALA* 2.7 47.1 + - + +
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Residues in contact with PRO 69 (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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53A VAL* 4.2 31.4 - - + -
54A GLY 5.1 1.6 - - - +
67A LEU 4.6 1.3 - - - +
68A LYS* 1.3 95.8 - - + +
70A ILE* 1.3 63.7 + - - +
71A GLY 3.8 1.3 - - - +
77A ILE* 5.7 4.9 - - + -
78A VAL 3.7 9.2 - - - +
79A CYS* 3.9 5.6 - - - -
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Residues in contact with ILE 70 (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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68A LYS* 3.3 23.1 - - - +
69A PRO* 1.3 80.9 - - - +
71A GLY* 1.3 62.9 + - - +
78A VAL* 3.0 35.3 + - + +
79A CYS 4.0 1.1 - - - +
80A ALA* 3.7 22.4 - - + +
91A ALA* 4.7 0.4 - - + -
148A LEU* 4.2 13.2 - - + -
501A 984 3.2 53.9 - - + +
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Residues in contact with GLY 71 (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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69A PRO* 5.2 1.0 - - - +
70A ILE* 1.3 83.3 - - - +
72A SER* 1.3 58.9 + - - -
77A ILE* 3.6 3.6 - - - +
78A VAL* 2.6 39.3 + - - +
501A 984 4.1 18.6 - - - -
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Residues in contact with SER 72 (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 GLY* 1.3 73.6 - - - -
73A GLY* 1.3 60.2 + - - +
76A GLY 3.5 9.6 - - - -
77A ILE* 3.7 20.9 - - - -
501A 984 3.4 20.7 - - - -
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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