Contacts of the strand formed by residues 107 - 112 (chain A) in PDB entry 4Y2H
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 ARG 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS 3.7 1.3 + - - +
85A THR* 3.1 19.1 - - + -
86A VAL 2.9 22.7 + - - -
105A ALA 3.3 0.8 - - - -
106A ARG* 1.3 86.1 + - + +
108A VAL* 1.3 72.0 + - - +
109A TYR* 3.6 40.3 + - + +
131A ASP* 3.7 14.3 + - - +
132A ARG 3.2 13.7 - - - -
134A HIS* 3.4 46.4 + - - -
146A PRO* 5.1 3.2 - - - +
147A GLU* 4.3 3.0 + - - +
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Residues in contact with VAL 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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86A VAL* 3.3 21.5 - - + +
88A ASP* 4.5 2.2 - - + -
97A SER* 3.8 46.7 - - - +
100A CYS* 3.9 8.1 - - + -
101A ALA* 4.2 6.7 - - + +
105A ALA* 3.8 21.3 - - + +
107A ARG* 1.3 81.5 - - - +
109A TYR* 1.3 71.8 + - - +
110A ALA 3.8 0.6 + - - +
132A ARG 2.7 13.7 + - - +
133A VAL* 3.5 9.9 - - + +
134A HIS* 2.9 29.1 + - - +
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Residues in contact with TYR 109 (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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85A THR* 4.6 3.1 - - - -
86A VAL 2.7 19.2 + - - +
87A LEU* 3.4 11.0 - - + +
88A ASP 2.8 31.0 + - - -
107A ARG* 3.6 33.7 + - + -
108A VAL* 1.3 74.4 - - - +
110A ALA* 1.3 56.8 + - - +
111A VAL* 3.7 0.7 - - - -
134A HIS* 3.6 16.2 - + + +
136A LEU* 4.4 15.7 - - + -
145A LEU* 4.1 22.2 - - + -
146A PRO* 3.2 40.8 - - + +
147A GLU* 2.6 40.4 + - + +
149A VAL* 3.9 18.6 - - + -
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Residues in contact with ALA 110 (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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88A ASP 3.9 1.6 - - - -
91A ALA* 3.5 18.8 - - + +
94A GLY* 5.5 2.0 - - - -
97A SER* 3.2 28.5 - - - +
108A VAL 3.8 0.6 + - - -
109A TYR* 1.3 69.5 - - - +
111A VAL* 1.3 63.3 + - - +
133A VAL* 4.1 9.9 - - + -
134A HIS 3.0 13.4 + - - +
135A VAL* 3.4 17.3 - - + +
136A LEU 2.8 24.5 + - - +
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Residues in contact with VAL 111 (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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87A LEU* 3.5 26.9 - - + -
88A ASP 2.9 12.2 + - - +
90A GLY 2.8 29.9 + - - +
91A ALA 2.8 6.8 + - - -
109A TYR 4.3 1.1 - - - +
110A ALA* 1.3 72.4 - - - +
112A GLU* 1.3 63.2 + - - +
136A LEU* 3.4 14.8 - - + +
138A GLY 3.6 17.0 - - - +
140A VAL* 3.9 29.2 - - + +
143A VAL* 4.2 26.9 - - + -
145A LEU* 4.2 9.2 - - + -
401A SAH 4.0 2.6 + - + -
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Residues in contact with GLU 112 (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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90A GLY 3.3 2.9 - - - -
91A ALA* 3.3 13.9 + - + +
92A GLY 2.6 29.5 + - - +
110A ALA 4.8 2.2 - - - +
111A VAL* 1.3 77.8 - - - +
113A ALA* 1.3 61.5 + - - +
114A SER* 2.9 26.2 + - - +
116A ILE* 3.5 22.4 - - + -
117A TRP* 3.8 22.6 - - + +
135A VAL* 5.1 1.8 - - + -
136A LEU 3.0 8.0 + - - +
137A PRO* 3.4 7.1 - - - +
138A GLY 3.0 20.0 + - - -
401A SAH 2.7 40.9 + - - -
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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