Contacts of the strand formed by residues 103 - 108 (chain A) in PDB entry 4Z7Q
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 VAL 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A HIS* 3.9 0.6 - - - -
99A SER* 3.4 6.9 + - - -
100A TRP* 3.0 44.4 + - + +
101A SER* 3.2 4.6 + - - -
102A ASP* 1.3 94.8 - - - +
104A ILE* 1.3 74.4 + - - +
105A VAL* 4.4 9.0 + - + +
132A LEU* 4.8 0.7 - - + -
133A ALA 3.4 12.8 - - - +
134A GLN* 4.7 11.4 - - + +
200A VAL* 4.2 17.5 - - + -
204A PHE* 4.0 24.0 - - + -
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Residues in contact with ILE 104 (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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26A HIS* 3.8 37.5 - - + +
36A VAL* 3.9 25.8 - - + -
53A VAL* 4.9 0.2 - - + -
55A LEU* 3.8 17.7 - - + -
68A LEU* 3.9 29.6 - - + -
70A PHE* 5.3 1.1 - - + -
97A VAL* 5.4 0.2 - - + -
98A VAL 3.7 6.1 - - - +
99A SER* 4.3 5.2 - - - +
103A VAL* 1.3 79.1 - - - +
105A VAL* 1.3 72.7 + - - +
106A ALA* 4.5 7.6 - - + +
131A PHE 3.7 1.2 - - - +
132A LEU* 3.3 5.0 - - - +
133A ALA* 3.0 35.1 + - + +
135A PRO* 4.0 9.6 - - + -
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Residues in contact with VAL 105 (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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96A SER 4.0 0.5 - - - +
97A VAL* 3.3 3.5 - - - +
98A VAL* 2.9 56.3 + - + +
100A TRP* 6.1 2.2 - - + +
103A VAL* 4.7 6.5 - - + +
104A ILE* 1.3 77.7 - - - +
106A ALA* 1.3 61.0 + - - +
107A CYS* 4.1 19.0 + - - -
130A CYS* 4.2 4.0 - - + -
131A PHE 3.6 3.4 - - - +
132A LEU* 3.8 30.1 - - + -
175A VAL* 4.8 6.1 - - + -
181A LEU* 4.0 33.0 - - + -
200A VAL* 5.3 4.5 - - + -
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Residues in contact with ALA 106 (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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53A VAL* 3.4 36.8 - - + -
70A PHE* 4.5 7.0 - - + -
93A LEU* 4.0 7.2 - - + -
94A GLY* 4.8 0.7 - - - -
96A SER 3.5 4.3 - - - -
97A VAL* 3.8 12.8 - - + -
104A ILE* 4.1 3.7 - - + +
105A VAL* 1.3 74.1 - - - +
107A CYS* 1.3 58.5 + - - +
131A PHE* 2.7 46.3 + - - +
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Residues in contact with CYS 107 (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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92A GLY 3.2 4.2 - - - +
93A LEU* 4.2 1.8 - - - -
94A GLY 3.0 21.2 + - - -
95A ALA 3.4 6.2 + - - -
96A SER* 3.0 27.4 + - - +
105A VAL* 4.1 10.8 - - - -
106A ALA* 1.3 77.6 - - - +
108A ALA* 1.3 60.9 + - - +
109A PRO* 3.5 2.6 - - - +
129A SER 3.5 3.8 - - - +
130A CYS* 2.0 45.1 - - - -
170A GLY* 3.5 21.1 - - - +
173A SER* 4.6 4.5 - - - -
183A LEU* 4.2 4.9 - - - -
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Residues in contact with ALA 108 (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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91A GLN* 3.4 42.6 - - + +
92A GLY 3.6 3.4 - - - -
93A LEU* 3.7 11.1 - - + +
107A CYS* 1.3 72.9 - - - +
109A PRO* 1.3 61.3 - - - +
110A TRP 3.0 10.2 + - - -
111A GLN* 3.2 7.7 + - + +
129A SER 2.8 29.6 + - - +
131A PHE* 4.3 8.3 - - + -
169A ALA 4.5 0.4 - - - -
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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