Contacts of the strand formed by residues 61 - 68 (chain A) in PDB entry 2HW6
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 ALA 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLU* 3.7 2.1 - - - +
58A GLY 2.7 36.5 + - - +
59A ALA 3.8 0.8 - - - -
60A TYR* 1.3 95.1 - - + +
62A LYS* 1.3 59.7 + - - +
78A LYS* 3.9 7.2 - - + -
79A ILE 3.1 11.9 - - - +
80A ILE* 3.9 13.0 - - + -
194A LEU* 3.1 26.2 + - + +
62B LYS* 5.6 1.5 - - - +
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Residues in contact with LYS 62 (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 LEU* 4.6 0.2 - - - +
54A LEU* 4.0 9.4 - - + -
56A GLY 3.2 14.1 - - - +
57A GLU* 3.3 33.1 + - + +
61A ALA* 1.3 75.4 - - - +
63A VAL* 1.3 65.4 + - - +
64A GLN* 2.8 28.5 + - - +
77A VAL 3.4 0.2 - - - +
78A LYS* 3.3 4.5 - - - +
79A ILE* 2.8 61.8 + - + +
119A ARG* 4.6 3.1 - - - +
194A LEU* 4.1 2.9 - - - -
58B GLY 4.3 10.7 + - - +
59B ALA 4.4 1.2 + - - -
60B TYR* 5.4 0.8 - - - +
61B ALA* 5.6 0.8 - - - +
81B GLU* 2.9 36.3 + - - +
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Residues in contact with VAL 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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54A LEU* 3.4 4.6 - - - +
55A LEU* 2.8 56.9 + - + +
56A GLY 2.8 11.3 + - - +
62A LYS* 1.3 77.4 - - - +
64A GLN* 1.3 56.8 + - - +
76A ALA* 4.2 11.2 - - + -
77A VAL 3.4 9.6 - - - +
78A LYS* 4.0 13.7 - - + +
192A PHE* 3.9 39.7 - - + -
194A LEU* 3.8 24.2 - - + -
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Residues in contact with GLN 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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50A LEU* 3.8 24.6 - - + +
51A THR 2.9 21.1 + - - +
53A GLU 3.5 13.5 - - - +
54A LEU* 4.1 8.9 - - + +
55A LEU* 4.0 5.8 - - - -
62A LYS* 2.8 35.6 + - + +
63A VAL* 1.3 75.7 - - - +
65A GLY* 1.3 74.2 + - - +
76A ALA* 3.6 1.0 - - - -
77A VAL* 2.8 36.1 + - - +
79A ILE* 4.6 5.6 - - + -
59B ALA* 2.9 35.3 + - - +
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Residues in contact with GLY 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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50A LEU* 3.3 5.9 - - - +
51A THR* 2.6 43.7 + - - -
53A GLU* 2.8 26.4 + - - -
55A LEU* 4.0 4.7 - - - +
64A GLN* 1.3 75.9 - - - +
66A ALA* 1.3 54.2 + - - -
74A GLU* 4.9 0.4 - - - -
75A TYR 3.5 10.1 - - - -
126A LYS* 4.8 3.1 - - - -
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Residues in contact with ALA 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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48A TYR* 4.1 20.0 - - + -
49A LYS 3.2 9.9 - - - +
50A LEU* 3.8 9.6 - - + -
51A THR* 4.1 1.3 - - - +
64A GLN 3.7 0.2 + - - -
65A GLY* 1.3 73.6 - - - +
67A VAL* 1.3 64.0 + - - +
68A SER 4.1 0.2 - - - -
74A GLU* 3.3 5.6 - - - +
75A TYR* 2.8 36.3 + - + +
77A VAL* 3.3 29.4 - - + -
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Residues in contact with VAL 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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48A TYR* 3.3 3.8 - - - -
49A LYS* 2.7 43.7 + - + +
51A THR* 3.6 21.1 - - + -
66A ALA* 1.3 76.3 - - - +
68A SER* 1.3 74.0 + - - +
69A LEU* 3.3 4.1 + - + +
72A GLY* 3.5 25.4 - - - +
73A LYS 3.5 4.3 - - - +
74A GLU* 4.6 11.4 - - + +
222B MET 5.9 0.7 - - - +
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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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47A MET 3.7 7.5 + - - -
48A TYR* 3.7 14.5 - - - -
67A VAL* 1.3 73.6 - - - +
69A LEU* 1.3 57.8 + - - +
70A GLN* 3.0 20.3 + - - +
71A ASN* 3.1 34.6 + - - -
72A GLY* 2.9 28.1 + - - -
73A LYS 2.9 13.4 + - - -
75A TYR* 3.8 12.1 - - - -
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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