Contacts of the strand formed by residues 125 - 129 (chain G) in PDB entry 4UNA
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 LEU 125 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G TYR* 3.5 7.2 - - - +
122G LEU* 3.6 39.7 - - + +
124G ARG* 1.3 75.6 - - - +
126G ARG* 1.3 60.0 + - - +
164G ASN* 3.9 1.3 + - - +
165G ILE* 2.7 69.6 + - + +
166G SER 4.9 0.2 - - - +
167G LEU* 4.1 15.5 - - + +
170G ARG* 3.7 41.1 - - + +
173G PHE* 4.0 19.1 - - + -
174G VAL* 4.5 6.7 - - + -
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Residues in contact with ARG 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G TYR* 3.4 6.8 + - - -
117G GLU 3.9 0.2 - - - +
118G GLY* 3.1 5.2 - - - -
119G ASP* 2.7 62.7 + - + +
124G ARG* 3.5 36.8 - - + +
125G LEU* 1.3 78.1 - - - +
127G ILE* 1.3 63.9 + - - +
128G TRP* 3.4 30.8 - - + +
154G ASP* 5.5 0.8 + - - -
162G VAL* 3.8 20.4 - - + -
163G LEU 3.3 4.7 - - - +
164G ASN* 3.3 26.2 - - - +
7H C 4.1 3.0 - - - +
8H C 4.8 2.0 - - - +
17O C 3.8 4.8 - - - +
18O G 3.0 46.3 + - - -
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Residues in contact with ILE 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G ILE* 4.8 12.1 - - + -
113G LEU* 4.0 32.8 - - + +
114G TYR* 3.5 29.8 - - + +
117G GLU* 3.7 13.5 - - + +
126G ARG* 1.3 76.8 - - - +
128G TRP* 1.3 69.0 + - - +
129G ASN* 5.7 0.2 - - + -
135G LEU* 4.1 11.5 - - + +
138G VAL* 4.5 22.0 - - + -
142G LEU* 5.3 0.7 - - + -
162G VAL* 3.4 3.0 - - - -
163G LEU* 2.8 46.3 + - + +
165G ILE* 4.1 17.3 - - + -
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Residues in contact with TRP 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G GLU* 3.1 50.5 + - - +
118G GLY 4.0 0.2 - - - -
119G ASP* 3.5 27.4 - - + -
126G ARG* 3.4 50.2 - - + +
127G ILE* 1.3 78.1 - - - +
129G ASN* 1.3 64.9 + - - +
154G ASP* 3.2 26.1 + - - -
155G ASP* 6.3 0.4 - - + -
160G VAL* 4.0 11.7 - - + -
161G TYR 3.5 6.1 - - - -
162G VAL* 3.6 20.4 - - + +
15I C 3.3 23.7 - - + +
16O C 3.4 54.5 - + + -
17O C 3.6 11.2 - + - +
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Residues in contact with ASN 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G ILE* 4.9 5.6 + - - +
113G LEU* 4.9 3.6 - - + +
117G GLU* 2.6 29.3 + - - -
127G ILE* 5.7 0.4 - - + -
128G TRP* 1.3 71.3 - - - +
130G LYS* 1.3 64.3 + - - +
131G ASN* 3.1 33.2 + - - +
134G LEU* 4.3 14.6 - - - +
135G LEU* 4.0 25.4 - - + +
160G VAL* 3.8 3.5 - - - +
161G TYR* 2.8 40.0 + - - +
1181G MN 3.8 2.6 + - - -
15I C 3.3 19.6 + - - -
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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
------------------------------------------------------------
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