Contacts of the strand formed by residues 73 - 82 (chain A) in PDB entry 2PMW
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 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ARG* 3.5 41.6 - - - +
67A CYS* 3.5 34.8 - - + +
69A LYS 3.9 1.8 - - - +
70A ASP* 3.0 44.6 + - - +
71A PRO 4.2 4.9 - - - +
72A TRP* 1.3 80.3 - - - +
74A LEU* 1.3 64.7 + - - +
75A PRO* 3.4 24.6 - - + +
145A GLU* 2.7 39.3 + - - +
146A ASP 4.2 2.9 - - - -
147A SER* 4.3 2.2 - - - -
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Residues in contact with LEU 74 (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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73A ARG* 1.3 79.8 - - - +
75A PRO* 1.3 69.6 - - - +
77A THR* 3.7 16.7 + - - +
145A GLU* 3.8 1.5 + - - +
146A ASP* 3.0 30.0 + - + +
147A SER* 3.6 22.9 - - - +
148A SER* 3.9 17.5 - - - +
209B PRO* 6.0 2.0 - - + -
258B LYS* 5.6 6.7 - - - +
260B THR* 3.4 33.0 - - + -
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Residues in contact with PRO 75 (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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73A ARG* 3.4 28.3 - - + +
74A LEU* 1.3 91.9 - - - +
76A GLY* 1.3 58.5 + - - +
77A THR* 5.0 0.7 + - - -
78A TYR* 4.7 3.4 - - - +
145A GLU* 3.3 24.2 - - + +
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Residues in contact with GLY 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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75A PRO* 1.3 75.2 - - - +
77A THR* 1.3 63.2 + - - +
78A TYR* 3.8 14.1 + - - -
125A LYS* 3.5 8.8 - - - +
126A MET 3.0 40.5 + - - +
127A SER* 5.5 1.6 - - - -
128A GLY 5.5 0.4 - - - -
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Residues in contact with THR 77 (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 LEU* 3.7 7.0 + - - +
75A PRO 3.3 3.7 + - - -
76A GLY* 1.3 82.3 + - - +
78A TYR* 1.3 70.2 + - - +
112A LEU* 4.2 13.0 - - + +
123A LEU* 3.5 30.7 - - + -
124A VAL 3.5 8.3 - - - +
125A LYS* 4.2 10.4 - - - +
145A GLU* 3.6 2.6 - - - +
146A ASP* 3.0 41.1 + - + +
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Residues in contact with TYR 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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64A PHE* 3.8 22.9 - + - -
75A PRO* 4.6 2.3 - - - +
76A GLY 3.8 21.4 + - - -
77A THR* 1.3 77.8 - - - +
79A VAL* 1.3 65.1 + - - +
80A VAL* 4.9 0.2 - - + -
122A PHE 3.8 0.3 - - - +
123A LEU* 3.4 4.7 - - - +
124A VAL* 3.0 42.3 + - + +
126A MET* 3.6 42.2 - - + -
127A SER 4.4 0.9 - - - -
128A GLY* 3.4 28.8 + - - -
131A LEU* 3.8 15.0 - - + +
143A ILE* 4.0 13.9 - - + -
144A GLU 3.5 2.2 - - - -
145A GLU* 3.6 41.3 + - + -
146A ASP 4.5 0.4 - - - +
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Residues in contact with VAL 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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78A TYR* 1.3 71.6 - - - +
80A VAL* 1.3 62.5 + - - +
81A VAL* 3.7 21.7 + - + +
115A PHE* 4.1 17.0 - - + -
119A LEU* 5.1 1.6 - - + -
122A PHE 3.7 3.1 - - - -
123A LEU* 3.8 19.7 - - + -
142A TYR 4.0 0.2 - - - +
143A ILE* 3.3 4.4 - - - -
144A GLU* 2.7 49.7 + - + +
146A ASP* 5.0 8.1 - - - +
261B VAL* 5.5 1.3 - - + -
262B SER* 4.3 10.3 - - - +
265B LEU* 4.1 19.7 - - + -
296B VAL* 4.0 17.0 - - + -
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Residues in contact with VAL 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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78A TYR* 4.5 0.7 - - + +
79A VAL* 1.3 74.6 - - - +
81A VAL* 1.3 60.7 + - - +
82A LEU* 4.2 14.6 - - + -
98A LEU* 5.0 3.6 - - + -
115A PHE* 5.2 0.2 - - - -
119A LEU* 5.3 0.2 - - - +
121A GLY* 3.1 7.6 - - - -
122A PHE* 2.8 72.3 + - + +
124A VAL* 4.0 19.1 - - + -
126A MET* 5.5 0.9 - - + -
134A ALA* 5.3 3.4 - - + +
137A LEU* 5.5 1.8 - - + -
140A VAL* 4.3 13.2 - - + -
142A TYR 4.0 1.6 - - - -
143A ILE* 4.0 31.4 - - + -
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Residues in contact with VAL 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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79A VAL* 3.8 10.8 - - + +
80A VAL* 1.3 75.2 - - - +
82A LEU* 1.3 66.0 + - - +
119A LEU* 3.7 25.6 - - + -
120A PRO 3.7 2.7 - - - -
140A VAL* 3.8 2.4 - - - +
141A ASP* 2.8 32.0 + - + +
142A TYR* 2.8 66.5 + - + +
296B VAL* 3.7 23.1 - - + -
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Residues in contact with LEU 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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80A VAL* 4.2 11.9 - - + -
81A VAL* 1.3 89.5 - - - +
83A LYS* 1.3 66.1 + - - +
84A GLU 3.6 1.0 + - - -
86A THR* 3.6 22.2 - - + +
91A SER* 3.4 42.0 - - - +
94A THR* 4.4 15.7 - - + +
120A PRO* 2.9 21.9 + - - +
121A GLY* 3.7 14.1 - - - -
122A PHE* 4.7 2.7 - - + -
138A PRO 4.5 1.6 - - - +
139A HIS* 3.1 18.2 - - + +
140A VAL* 3.8 21.3 - - + +
141A ASP* 3.8 5.4 - - - +
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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