Contacts of the strand formed by residues 59 - 66 (chain A) in PDB entry 4HZF
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 GLU 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.1 31.8 - - + +
52A ILE 3.3 4.9 - - - +
53A LYS* 3.6 28.1 + - + -
57A GLY 3.5 14.8 - - - +
58A LYS* 1.3 72.0 - - - +
60A MET* 1.3 60.7 + - - +
61A ILE 4.3 0.2 - - - -
175A GLN* 3.5 32.3 + - - +
302A CMP 3.1 34.4 + - - +
137B PHE* 4.2 0.4 - - - -
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Residues in contact with MET 60 (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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51A LEU* 3.4 4.3 - - - +
52A ILE* 2.9 51.7 + - + -
59A GLU* 1.3 73.8 - - - +
61A ILE* 1.3 74.7 + - - +
62A LEU* 3.6 1.3 + - + +
131A LYS* 5.1 1.3 - - - -
135A LEU* 4.6 4.7 - - + -
175A GLN 3.0 26.0 - - - +
176A ILE 3.7 9.2 - - - +
177A VAL 4.4 0.7 - - - -
178A GLY* 3.7 24.9 - - - +
302A CMP 4.7 1.3 - - + -
132B VAL* 3.5 28.0 - - + -
133B GLY* 5.0 0.2 - - - -
136B ALA* 3.8 20.9 - - + -
137B PHE* 3.6 19.9 - - + -
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Residues in contact with ILE 61 (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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49A ALA* 4.4 7.2 - - + -
50A VAL 3.5 5.6 - - - +
51A LEU* 3.8 22.0 - - + -
60A MET* 1.3 81.6 - - - +
62A LEU* 1.3 60.6 + - - +
63A SER 3.7 25.8 - - - +
64A TYR* 4.0 34.1 - - + +
131A LYS* 4.5 10.9 + - - +
172A GLU* 4.4 7.6 - - + +
175A GLN* 2.8 43.4 + - + +
176A ILE* 4.1 17.2 - - + -
304A GOL 4.3 9.0 + - - +
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Residues in contact with LEU 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 VAL* 2.8 25.4 + - + +
52A ILE* 3.7 36.6 - - + -
60A MET* 3.6 1.5 + - + +
61A ILE* 1.3 73.1 - - - +
63A SER* 1.3 61.1 + - - +
85A ALA* 4.5 1.3 - - + -
127A VAL* 5.6 2.8 - - - +
128A THR* 4.7 4.7 + - + +
131A LYS* 3.5 24.5 + - + -
301A CMP 3.7 37.4 + - + +
304A GOL 4.4 1.4 + - - -
129B SER* 3.8 24.0 - - - +
132B VAL* 3.8 36.8 - - + -
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Residues in contact with SER 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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49A ALA* 3.5 2.8 - - - -
50A VAL* 2.8 32.9 + - - +
61A ILE* 3.5 8.1 - - - +
62A LEU* 1.3 82.5 - - - +
64A TYR* 1.3 81.1 + - - +
65A LEU* 3.7 8.5 - - - +
124A ARG* 5.6 0.2 - - - +
127A VAL* 5.8 4.6 - - - +
301A CMP 3.5 29.9 - - - -
304A GOL 4.1 7.6 - - - -
305A GOL 4.8 4.2 + - - -
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Residues in contact with TYR 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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48A VAL 3.3 8.1 - - - +
49A ALA* 3.9 17.0 - - + -
61A ILE* 4.0 19.7 - - + +
63A SER* 1.3 87.1 + - - +
65A LEU* 1.3 65.5 + - - +
66A ASN* 4.4 13.5 + - - +
69A ASP* 4.8 0.2 - - - +
90A LYS* 3.5 41.7 - - + +
151A LEU* 4.8 11.7 - - + -
154A GLN* 6.6 0.2 - - + -
168A ILE* 4.5 5.0 - - - +
172A GLU* 4.3 13.0 + - - +
176A ILE* 3.6 23.3 - - + +
304A GOL 3.3 32.6 + - - -
305A GOL 5.0 2.1 + - - -
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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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43A ILE* 4.0 5.2 - - + -
47A SER* 3.2 4.3 - - - -
48A VAL* 2.8 42.9 + - + -
50A VAL* 3.7 24.9 - - + -
63A SER* 3.7 8.7 - - - +
64A TYR* 1.3 82.9 - - - +
66A ASN* 1.3 66.9 + - - +
69A ASP* 3.3 15.5 - - + +
70A PHE 4.1 6.3 - - - +
71A ILE* 4.2 15.7 - - + -
124A ARG* 3.8 22.0 - - - +
301A CMP 4.0 12.1 - - + +
305A GOL 3.4 31.6 - - - -
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Residues in contact with ASN 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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43A ILE* 3.6 8.7 - - - +
46A GLY 3.6 9.9 - - - +
47A SER* 3.1 23.9 - - - -
64A TYR* 4.4 10.3 + - - +
65A LEU* 1.3 82.7 + - - +
67A GLN* 1.3 72.1 + - + +
69A ASP* 2.7 30.6 + - - +
90A LYS* 4.7 3.3 + - - -
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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