Contacts of the strand formed by residues 66 - 72 (chain A) in PDB entry 1Q2L
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 SER 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LYS* 1.3 74.1 - - - +
67A LEU* 1.3 60.9 + - - +
132A GLU* 3.2 3.5 - - - +
133A VAL* 2.9 36.3 + - - +
135A ASN* 2.9 23.3 + - - +
138A LEU* 3.5 29.4 - - - -
236A TYR 3.0 12.6 - - - -
237A SER* 2.9 28.5 + - - +
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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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65A LYS* 4.2 10.1 - - + +
66A SER* 1.3 78.1 - - - +
68A SER* 1.3 62.7 + - - +
131A LEU* 3.4 11.2 - - - +
132A GLU* 3.4 33.2 - - + +
138A LEU* 4.5 4.6 - - - +
235A ILE* 3.7 1.0 - - - -
236A TYR* 2.8 55.0 + - + +
407A ARG* 3.8 20.4 - - + +
408A ASP* 3.4 39.7 - - - +
409A MET 3.7 0.9 - - - +
411A TYR* 4.7 1.8 - - + -
412A VAL* 3.3 25.1 - - + -
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Residues in contact with SER 68 (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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67A LEU* 1.3 79.5 - - - +
69A ALA* 1.3 61.7 + - - +
130A TYR* 3.2 2.9 - - - +
131A LEU* 2.8 52.6 + - - +
138A LEU* 4.7 0.4 - - - -
142A VAL* 3.9 19.4 - - - +
145A LEU* 4.2 3.6 - - - +
234A VAL 2.9 19.0 + - - -
235A ILE* 4.2 2.3 - - - +
252A PHE* 3.7 22.3 - - - -
412A VAL* 3.9 4.1 - - - +
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Residues in contact with ALA 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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68A SER* 1.3 79.4 + - - +
70A LEU* 1.3 61.2 + - - +
71A VAL* 5.5 0.2 - - + -
129A PHE 3.1 12.1 - - - +
130A TYR* 3.7 12.8 - - + -
145A LEU* 4.7 3.6 - - - -
233A ALA* 3.0 6.9 - - - +
234A VAL* 2.8 33.6 + - + +
252A PHE* 4.4 0.3 - - - -
412A VAL* 3.8 27.6 - - + +
413A GLU* 4.4 1.3 - - - +
416A ALA* 4.0 11.7 - - + -
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Residues in contact with LEU 70 (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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53A MET* 4.0 11.9 - - + -
69A ALA* 1.3 75.7 - - - +
71A VAL* 1.3 64.5 + - - +
72A VAL* 3.9 24.7 - - + -
128A ALA* 3.5 1.7 - - - -
129A PHE* 2.9 34.8 + - + +
145A LEU* 4.5 11.0 - - + +
149A ILE* 4.0 30.5 - - + -
231A MET* 3.9 27.6 - - + -
232A LYS 3.3 15.7 - - - +
233A ALA* 3.8 12.3 - - + -
252A PHE* 4.2 17.3 - - + -
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Residues in contact with VAL 71 (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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69A ALA* 5.5 0.9 - - + -
70A LEU* 1.3 75.8 - - - +
72A VAL* 1.3 75.2 + - - +
73A PRO* 4.0 1.2 - - - +
126A ARG* 4.0 16.6 - - + -
127A THR 3.4 8.3 - - - +
128A ALA* 3.4 24.5 - - + -
231A MET* 3.3 7.8 - - - +
232A LYS* 2.7 35.6 + - + +
413A GLU* 4.9 0.2 - - - +
416A ALA* 3.3 34.1 - - + +
417A ASP* 3.6 11.0 - - - +
420A ILE* 3.9 20.4 - - + -
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Residues in contact with VAL 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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70A LEU* 3.9 17.7 - - + -
71A VAL* 1.3 78.5 - - - +
73A PRO* 1.3 61.8 - - + +
74A VAL* 2.7 30.1 + - + +
126A ARG* 3.3 2.4 - - - +
127A THR* 2.9 36.6 + - - +
129A PHE* 4.6 2.7 - - + -
225A TYR 3.7 23.3 - - - +
226A TYR* 4.1 32.1 - - + -
230A LEU* 5.7 0.7 - - + -
231A MET* 3.9 20.9 - - + -
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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