Contacts of the strand formed by residues 62 - 67 (chain A) in PDB entry 4Q1U
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 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A GLU 4.0 0.2 - - - +
57A ILE* 3.4 0.8 - - - -
58A LEU* 2.6 46.1 + - + +
60A ASN* 3.0 26.4 + - - +
61A GLY* 1.3 78.9 - - - +
63A ALA* 1.3 57.3 + - - +
64A PHE* 5.2 0.4 - - - -
87A LEU* 4.1 21.8 - - + -
88A MET 3.5 2.5 - - - +
89A ASP* 3.8 37.0 - - + +
146A PHE* 3.8 31.6 - - + -
148A GLU* 3.9 23.6 - - + +
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Residues in contact with ALA 63 (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* 5.8 0.4 - - + -
56A GLU 3.4 5.4 - - - +
57A ILE* 4.0 20.2 - - + +
62A LEU* 1.3 75.1 - - - +
64A PHE* 1.3 64.6 + - - +
65A ILE* 4.5 3.2 - - + +
86A LEU 3.7 0.2 - - - +
87A LEU* 3.3 9.0 - - - +
88A MET* 2.9 43.0 + - + +
90A LEU* 4.0 16.2 - - + -
342A LEU* 4.3 12.3 - - + -
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Residues in contact with PHE 64 (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* 2.9 8.3 - - - +
56A GLU 2.8 39.9 + - - +
58A LEU* 3.7 30.5 - - + -
62A LEU 4.9 0.7 - - - -
63A ALA* 1.3 72.1 - - - +
65A ILE* 1.3 64.6 + - - +
85A ILE* 4.1 9.4 - - + -
86A LEU 3.4 1.6 - - - +
87A LEU* 4.0 10.1 - - + -
100A LEU* 3.6 32.8 - - + -
117A ILE* 3.6 17.4 - - + +
119A THR* 4.1 18.4 - - + -
127A VAL* 4.6 2.9 - - + -
129A LEU* 4.2 14.1 - - + -
146A PHE* 3.6 44.6 - + + -
153A LEU* 4.4 6.7 - - + -
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Residues in contact with ILE 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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48A ILE* 4.1 14.4 - - + -
52A SER* 3.6 31.6 - - - -
54A ASP 3.5 7.6 - - - +
55A LEU* 3.8 15.0 - - + -
63A ALA* 4.5 4.9 - - + +
64A PHE* 1.3 82.9 - - - +
66A SER* 1.3 66.4 + - - +
84A LYS 3.8 0.2 - - - +
85A ILE* 3.3 5.6 - - - -
86A LEU* 2.7 55.9 + - + +
88A MET* 3.7 35.0 - - + -
97A VAL* 4.6 2.7 - - + -
117A ILE* 4.8 1.3 - - - -
342A LEU* 4.3 12.8 - - + -
350A ALA* 5.6 1.3 - - + -
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Residues in contact with SER 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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52A SER* 3.2 22.9 - - - -
53A GLU* 3.3 6.6 + - - +
54A ASP* 3.0 19.1 + - - +
65A ILE* 1.3 73.7 - - - +
67A SER* 1.3 59.9 + - - +
84A LYS 3.5 5.2 - - - -
85A ILE* 3.8 18.4 - - - -
114A PRO* 3.9 13.0 + - - -
115A HIS* 2.8 29.1 + - - -
117A ILE* 3.9 11.9 - - - +
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Residues in contact with SER 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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50A ASN* 4.3 4.3 - - - -
51A GLY 2.9 26.2 - - - -
53A GLU* 5.0 1.1 - - - +
66A SER* 1.3 74.2 - - - +
68A GLY* 1.3 66.2 + - - +
69A LEU* 3.1 4.9 - - - +
82A SER 5.7 0.2 - - - -
83A GLY* 3.5 0.2 - - - -
84A LYS* 2.9 42.8 + - - +
86A LEU* 3.5 27.0 - - - +
114A PRO* 3.3 10.5 - - - +
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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