Contacts of the strand formed by residues 113 - 118 (chain D) in PDB entry 3HU1
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 113 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LYS* 1.3 90.4 - - + +
114D ILE* 1.3 65.5 + - - +
167D GLU* 4.7 0.7 - - - +
168D THR* 3.7 1.0 - - - -
169D ASP* 2.8 48.4 + - + +
170D PRO* 4.7 0.2 - - - +
180D THR* 4.5 0.2 - - - -
181D VAL* 3.6 18.8 - - + +
183D HIS* 3.2 41.1 + - + -
185D GLU* 5.8 0.4 + - - -
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Residues in contact with ILE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ARG* 1.3 79.5 - - - +
115D HIS* 1.3 60.6 + - - +
116D VAL* 4.1 19.3 - - + -
139D PHE* 4.5 8.5 - - + -
146D ILE* 3.9 28.3 - - + -
165D VAL* 5.4 0.2 - - + -
167D GLU 3.5 6.5 - - - +
168D THR* 4.1 9.6 - - + -
174D CYS* 3.9 28.3 - - - -
176D VAL* 4.3 11.7 - - + -
180D THR* 4.1 14.3 - - + +
181D VAL 3.1 14.8 + - - +
182D ILE* 4.1 24.7 - - + -
183D HIS* 2.9 32.8 + - - +
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Residues in contact with HIS 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ILE* 1.3 72.9 - - - +
116D VAL* 1.3 61.0 + - - +
117D LEU* 3.8 35.0 - - + +
165D VAL* 3.7 2.1 - - - +
166D VAL* 2.8 44.4 + - + -
167D GLU* 3.1 31.1 + - + +
183D HIS* 3.4 8.0 - - + +
185D GLU* 3.2 42.3 + - + -
186D GLY* 4.1 3.9 + - - -
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ILE* 4.1 19.7 - - + -
115D HIS* 1.3 79.7 - - - +
117D LEU* 1.3 67.8 + - - +
135D LEU* 3.7 35.2 - - + -
139D PHE* 5.5 0.7 - - + -
152D PHE* 4.1 22.9 - - + -
163D PHE* 4.7 9.0 - - + -
164D LYS 3.3 11.0 - - - +
165D VAL* 4.1 9.6 - - + -
182D ILE* 4.1 10.3 - - + -
183D HIS 2.9 15.4 + - - +
184D CYS* 3.2 27.5 - - + +
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D HIS* 3.8 16.6 - - + +
116D VAL* 1.3 82.4 - - - +
118D PRO* 1.4 75.0 - - + +
119D ILE* 4.4 0.2 - - - +
163D PHE* 3.3 5.1 - - - -
164D LYS* 2.8 36.9 + - - +
166D VAL* 3.9 22.4 - - + -
184D CYS 4.2 7.6 - - - +
186D GLY* 3.5 42.2 - - - +
187D GLU 3.7 16.4 - - - +
189D ILE* 4.0 23.4 - - + +
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Residues in contact with PRO 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D VAL 4.9 0.4 - - - +
117D LEU* 1.4 93.8 - - + +
119D ILE* 1.3 62.9 + - - +
120D ASP 3.6 0.3 + - - -
123D VAL* 4.2 22.0 - - + -
130D LEU* 4.2 22.4 - - + -
161D VAL* 3.9 14.4 - - + -
162D GLU 3.3 7.6 - - - +
163D PHE* 3.7 20.1 - - + -
184D CYS* 5.5 5.8 - - + +
186D GLY 5.7 1.3 - - - +
188D PRO* 3.7 12.8 - - + +
189D ILE* 3.0 25.6 + - - -
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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
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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