Contacts of the strand formed by residues 96 - 100 (chain D) in PDB entry 3LHD
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 96 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLY 3.9 1.3 + - - +
95D ASP* 1.3 71.2 - - - +
97D ILE* 1.3 66.6 + - - +
98D VAL* 4.8 3.1 - - + -
120D ARG* 3.5 23.6 - - + +
122D VAL* 3.6 26.5 - - + -
160D GLU* 3.5 32.8 - - + -
161D GLU 3.7 18.4 - - - -
162D ASN 3.9 17.3 - - - +
163D VAL* 3.7 9.3 - - + -
164D ASP* 2.7 48.3 + - - +
165D HIS 3.5 0.3 + - - -
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Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ILE* 3.5 27.1 - - + -
95D ASP* 4.4 2.0 - - + -
96D PHE* 1.3 80.7 - - - +
98D VAL* 1.3 76.2 + - - +
99D GLU* 4.1 3.3 + - + +
111D LEU* 4.2 23.3 - - + -
115D VAL* 3.4 31.2 - - + -
120D ARG 2.9 12.6 + - - +
121D VAL* 3.4 8.6 - - + -
122D VAL* 2.9 25.8 + - - -
165D HIS* 3.4 25.8 - - + +
167D ILE* 3.8 19.1 - - + -
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PHE* 4.4 2.7 + - + -
97D ILE* 1.3 78.4 - - - +
99D GLU* 1.3 61.9 + - - +
122D VAL* 3.4 6.1 - - + +
124D TYR* 4.0 15.7 - - + -
154D ILE* 3.9 26.2 - - + -
158D ILE* 4.2 15.7 - - + -
160D GLU* 4.0 25.4 - - + +
163D VAL* 3.9 25.6 - - + -
165D HIS 2.8 12.2 + - - +
166D VAL* 3.2 13.2 - - + +
167D ILE 2.7 25.3 + - - -
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Residues in contact with GLU 99 (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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97D ILE* 4.1 6.8 + - + -
98D VAL* 1.3 78.9 - - - +
100D ALA* 1.3 60.3 + - - +
101D GLY 3.0 37.4 - - - +
102D VAL* 3.1 8.0 + - - +
107D LEU* 4.0 21.7 - - - +
108D THR* 3.2 21.2 + - - +
111D LEU* 4.8 6.5 - - + -
121D VAL* 4.3 9.0 - - + -
122D VAL 2.9 7.9 + - - +
123D SER* 2.9 28.5 - - - +
124D TYR* 2.8 24.1 + - - -
167D ILE* 3.1 23.7 - - + +
168D LEU* 5.3 0.2 - - - -
169D ASP* 5.1 0.2 - - - -
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Residues in contact with ALA 100 (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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99D GLU* 1.3 75.7 - - - +
101D GLY* 1.3 62.3 + - - +
124D TYR* 3.6 10.3 - - + +
154D ILE* 3.4 46.4 - - + -
167D ILE 3.3 4.9 + - - +
168D LEU* 3.7 8.1 - - + +
169D ASP* 3.2 26.2 + - - +
170D LEU* 3.6 13.3 - - + +
301D SAH 4.2 1.3 - - + -
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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