Contacts of the strand formed by residues 114 - 120 (chain A) in PDB entry 6DU3
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 PHE 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A VAL* 5.1 0.2 - - + -
112A ALA* 3.9 2.3 - - - +
113A ASP* 1.3 92.9 - - + +
115A ILE* 1.3 67.6 + - - +
116A ILE* 4.7 2.9 - - + -
128A TYR* 3.8 0.2 - - - -
129A VAL* 2.8 62.6 + - + +
131A LYS* 3.7 37.9 - - + -
162A VAL* 4.6 9.6 - - + -
165A LEU* 3.6 62.1 - - + -
166A LEU* 4.2 15.7 - - + -
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Residues in contact with ILE 115 (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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109A VAL 5.5 0.4 - - - +
112A ALA* 4.2 9.2 - - + -
114A PHE* 1.3 79.3 - - - +
116A ILE* 1.3 68.1 + - - +
117A PRO* 4.1 5.2 - - + +
126A GLN* 3.4 39.3 - - + +
127A VAL 3.3 6.3 - - - +
128A TYR* 3.6 34.3 - - + -
165A LEU* 5.6 1.2 - - - +
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Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 4.7 7.9 - - + -
115A ILE* 1.3 80.5 - - - +
117A PRO* 1.3 73.5 - - + +
118A VAL* 3.5 22.9 + - + -
126A GLN* 4.1 2.2 - - - -
127A VAL* 2.9 38.1 + - + +
129A VAL* 4.7 6.1 - - + -
157A LYS 4.9 0.2 - - - +
158A TYR* 4.8 4.0 - - + +
161A PRO* 3.4 30.7 - - + +
162A VAL* 3.3 49.8 - - + +
165A LEU* 4.7 10.3 - - + -
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Residues in contact with PRO 117 (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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115A ILE 4.1 5.2 - - - +
116A ILE* 1.3 89.7 - - + +
118A VAL* 1.3 63.2 + - - +
119A GLU 4.2 0.7 + - - -
124A VAL* 3.6 22.2 - - + -
125A HIS 3.5 6.5 - - - +
126A GLN* 3.6 17.2 - - - +
157A LYS 5.1 1.9 - - - +
161A PRO* 6.0 0.2 - - - +
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Residues in contact with VAL 118 (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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106A PHE* 5.0 1.1 - - + -
116A ILE* 3.6 26.0 - - + +
117A PRO* 1.3 76.8 - - - +
119A GLU* 1.3 66.8 + - - +
120A ILE* 3.5 21.2 + - + +
124A VAL* 4.0 1.9 - - - +
125A HIS* 2.9 31.1 + - - +
127A VAL* 3.8 22.7 - - + -
157A LYS* 4.0 28.5 - - + +
158A TYR* 4.2 23.3 - - + -
860C LEU* 6.3 0.7 - - + -
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Residues in contact with GLU 119 (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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117A PRO 4.2 1.2 + - - -
118A VAL* 1.3 71.5 - - - +
120A ILE* 1.3 66.2 + - - +
121A ASP 4.4 1.0 + - - +
122A GLY* 3.6 35.9 + - - +
123A VAL 3.6 4.9 - - - -
124A VAL* 4.0 17.6 - - + +
157A LYS* 3.1 33.7 + - + +
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Residues in contact with ILE 120 (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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106A PHE* 3.2 41.1 - - + -
118A VAL* 3.5 15.5 + - + +
119A GLU* 1.3 79.5 - - - +
121A ASP* 1.3 82.5 + - - +
123A VAL* 2.9 26.9 + - - +
125A HIS* 4.3 12.0 + - + +
157A LYS* 4.8 6.3 - - + +
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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