Contacts of the strand formed by residues 104 - 109 (chain A) in PDB entry 4DF3
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 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ASP 3.0 7.3 + - - +
80A ARG* 3.3 33.8 - - - +
81A ILE* 2.8 26.9 + - - +
99A ILE* 3.5 8.0 - - - +
102A ARG 4.9 0.2 - - - +
103A GLY* 1.3 80.3 - - - +
105A ILE* 1.3 60.6 + - - +
106A TYR* 3.3 39.2 + - + -
127A ASN 3.3 7.4 - - - +
129A PHE* 3.3 46.8 - - + -
146A GLU* 4.0 4.4 + - - -
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 3.4 12.8 - - + +
83A TYR* 3.7 33.7 - - + -
86A ILE* 4.4 10.5 - - + -
92A ALA* 3.3 32.1 - - + +
95A MET* 3.6 19.7 - - + -
96A SER* 3.6 12.8 - - - +
99A ILE* 3.6 13.2 - - + -
104A ARG* 1.3 74.0 - - - +
106A TYR* 1.3 63.4 + - - +
107A GLY 3.4 2.4 + - - +
127A ASN 2.9 11.7 + - - +
128A ILE* 3.6 11.4 - - + +
129A PHE* 2.7 33.3 + - - +
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Residues in contact with TYR 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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80A ARG* 4.6 3.6 - - + -
81A ILE 2.7 20.1 + - - +
82A LEU* 3.7 9.6 - - + +
83A TYR* 2.8 33.4 + - - +
104A ARG* 3.3 34.9 + - + -
105A ILE* 1.3 73.0 - - - +
107A GLY* 1.3 56.5 + - - +
108A VAL 3.7 0.5 + - - -
129A PHE* 3.4 28.7 - + + -
131A ILE* 4.2 9.0 - - + -
144A LEU 3.2 26.9 - - - -
145A VAL* 4.1 20.9 - - + -
146A GLU* 2.7 51.1 + - + +
148A VAL* 4.1 17.7 - - + -
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Residues in contact with GLY 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR* 3.6 6.5 - - - -
86A ILE* 3.5 34.9 - - - +
105A ILE* 3.4 3.0 + - - -
106A TYR* 1.3 71.5 - - - +
108A VAL* 1.3 61.5 + - - -
109A GLU 3.8 0.2 + - - -
115A MET* 4.3 1.0 - - - +
129A PHE 2.8 13.6 + - - -
130A PRO* 3.4 5.7 - - - +
131A ILE* 2.8 27.2 + - - +
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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
----------------------------------------------------------
82A LEU* 3.8 28.0 - - + -
83A TYR 2.8 12.5 + - - +
84A LEU* 3.9 11.4 - - + -
85A GLY 2.8 29.5 + - - -
86A ILE 3.2 4.9 + - - -
106A TYR 4.5 0.7 - - - +
107A GLY* 1.3 71.9 - - - -
109A GLU* 1.3 59.7 + - - +
131A ILE* 3.4 19.1 - - + +
133A GLY* 3.3 26.0 - - - +
135A ALA* 3.9 20.9 - - + +
141A TYR* 3.9 25.6 - - + +
301A SAM 4.1 3.4 + - + -
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Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE* 3.9 14.6 + - + -
87A ALA 3.0 20.4 + - - +
108A VAL* 1.3 76.3 - - - +
110A PHE* 1.3 61.5 + - - +
111A ALA* 3.0 30.9 + - - +
114A VAL* 3.7 18.2 - - + -
115A MET* 3.9 19.2 - - + +
131A ILE 3.1 8.0 + - - +
132A LEU* 3.4 9.9 - - - +
133A GLY 3.1 18.4 + - - -
301A SAM 2.6 57.4 + - - -
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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