Contacts of the strand formed by residues 63 - 69 (chain A) in PDB entry 4H1U
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU* 5.3 0.4 - - + -
51A LEU* 3.6 31.6 - - + -
61A ARG 3.6 3.6 + - - +
62A PRO* 1.3 72.5 - - - +
64A ILE* 1.3 64.8 + - - +
65A LEU* 3.2 22.8 + - + +
111A ILE* 4.4 16.8 - - + -
130A ILE* 3.5 39.0 - - + +
132A LEU* 4.1 20.2 - - + -
144A LEU 3.4 0.2 - - - +
145A VAL* 4.6 0.7 - - - -
146A ASP* 2.8 53.0 + - + +
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Residues in contact with ILE 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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12A GLN* 3.6 40.4 - - + +
27A GLN* 5.3 1.6 - - - +
63A LEU* 1.3 70.7 - - - +
65A LEU* 1.3 58.7 + - - +
66A GLN* 3.6 17.9 + - + +
129A PRO* 3.8 22.7 - - + -
130A ILE 2.7 13.0 + - - +
131A HIS* 3.3 33.9 - - + +
132A LEU* 3.0 28.8 + - - +
143A THR* 4.2 4.9 - - + -
144A LEU 3.7 3.8 - - - +
145A VAL* 4.3 19.3 - - + +
173A PHE* 6.1 0.9 - - + -
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Residues in contact with LEU 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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42A LEU* 4.5 28.3 - - + +
46A VAL* 3.9 24.9 - - + -
50A LEU* 4.1 7.6 - - + -
51A LEU* 5.1 2.2 - - + -
63A LEU* 3.2 17.9 + - + +
64A ILE* 1.3 70.0 - - - +
66A GLN* 1.3 60.2 + - - +
67A LEU* 3.8 13.3 + - + +
132A LEU* 3.8 33.7 - - + +
134A ILE* 3.8 20.4 - - + -
142A LEU 3.9 0.7 - - - +
143A THR* 3.4 3.0 - - - -
144A LEU* 2.8 45.5 + - + +
146A ASP* 5.9 0.4 - - + -
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Residues in contact with GLN 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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9A ASN* 3.4 37.6 + - - +
12A GLN* 2.9 24.2 + - - +
13A ASP* 3.6 10.8 + - - +
64A ILE* 3.8 15.2 - - + +
65A LEU* 1.3 73.0 - - - +
67A LEU* 1.3 64.9 + - - +
68A VAL* 3.4 3.6 + - + +
131A HIS* 5.1 2.3 - - - +
132A LEU 2.8 17.2 + - - +
133A LYS* 2.8 39.7 + - + +
134A ILE 2.9 25.5 + - - -
143A THR* 3.5 22.9 - - + +
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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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5A ILE* 5.6 1.7 - - - +
45A LEU* 4.0 37.5 - - + +
46A VAL* 3.8 23.6 - - + +
65A LEU* 3.9 18.8 - - + +
66A GLN* 1.3 69.8 - - - +
68A VAL* 1.3 61.1 + - - +
69A HIS 4.0 0.2 - - - -
134A ILE* 3.6 25.1 - - + -
139A VAL* 4.0 15.9 - - + -
140A VAL* 3.7 16.2 - - + +
141A ASN* 3.5 7.6 - - - +
142A LEU* 2.8 48.2 + - + +
143A THR* 5.4 0.2 + - - -
144A LEU* 6.0 2.7 - - + -
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Residues in contact with VAL 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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6A PRO* 6.3 3.6 - - + -
9A ASN* 4.3 17.9 - - - +
66A GLN* 3.9 10.5 - - + +
67A LEU* 1.3 75.0 - - - +
69A HIS* 1.3 72.0 + - - +
70A VAL* 3.9 1.4 - - + +
133A LYS* 4.9 8.7 - - + -
134A ILE 2.8 13.5 + - - +
135A PHE* 3.3 37.1 - - + -
136A SER 3.1 23.4 + - - -
139A VAL* 3.9 2.2 - - - -
141A ASN* 3.8 6.5 - - - +
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Residues in contact with HIS 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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67A LEU 3.9 1.4 + - - -
68A VAL* 1.3 79.7 - - - +
70A VAL* 1.3 93.1 + - - +
71A SER* 4.6 2.4 + - - -
136A SER 3.2 10.6 + - - -
137A PRO* 3.2 23.7 + - + -
138A ASN 5.5 0.2 - - - -
139A VAL* 2.8 28.8 + - - +
140A VAL* 4.7 0.9 - - - -
141A ASN* 2.9 33.0 + - - +
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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