Contacts of the strand formed by residues 116 - 123 (chain D) in PDB entry 3HW4
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 116 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D VAL* 5.4 2.9 - - - -
110D TYR* 3.4 10.0 - - - -
111D ASP* 2.8 34.5 + - + +
114D GLU* 3.2 47.9 + - + +
115D ASN* 1.3 76.0 - - - +
117D PHE* 1.3 63.1 + - - +
118D ILE* 4.6 5.2 - - - -
142D LYS* 3.8 16.2 - - + +
144D HIS* 3.3 46.0 + - - -
160D ASP* 3.0 29.3 + - - -
162D THR* 3.5 19.0 + - - -
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Residues in contact with PHE 117 (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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79D ILE* 3.8 16.4 - - + -
91D VAL* 4.1 13.5 - - + -
94D ILE* 3.9 20.0 - - + -
95D CYS* 4.1 15.0 - - - -
100D VAL* 4.3 11.4 - - + -
101D GLU 3.8 13.9 - - - -
103D PRO* 3.7 25.8 - - + -
107D PRO* 3.5 31.4 - - + -
109D LEU 3.4 9.2 - - - +
110D TYR* 3.5 27.4 - + + -
116D ARG* 1.3 77.7 - - - +
118D ILE* 1.3 61.9 + - - +
142D LYS 4.1 4.9 + - - -
143D THR* 3.6 16.9 - - - +
144D HIS* 3.0 25.5 + - - +
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Residues in contact with ILE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TYR* 4.0 19.5 - - + +
76D PHE* 3.7 32.3 - - + -
107D PRO* 4.4 0.4 - - - -
108D ASP* 2.8 32.3 + - - +
109D LEU* 2.8 29.0 + - + +
111D ASP* 3.8 15.9 - - + +
116D ARG* 4.2 7.9 - - - +
117D PHE* 1.3 80.7 - - - +
119D GLU* 1.3 64.2 + - - +
120D ILE* 3.9 21.1 - - + -
143D THR* 4.0 4.5 - - - -
144D HIS* 3.3 24.0 - - + +
146D HIS* 4.6 4.7 - - + -
162D THR* 4.4 7.0 - - + +
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Residues in contact with GLU 119 (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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106D LEU 4.1 4.3 - - - +
107D PRO* 4.0 13.2 - - - +
108D ASP* 2.9 16.3 - - - +
118D ILE* 1.3 74.2 - - - +
120D ILE* 1.3 60.0 + - - +
134D LYS* 2.9 43.2 + - + +
137D LYS* 5.8 1.8 + - - -
138D ILE* 4.3 20.9 - - + +
143D THR* 3.7 13.3 - - + +
144D HIS 2.8 13.2 + - - +
145D ILE* 3.4 8.8 - - + +
146D HIS 3.0 25.6 + - - -
257D TMP 2.9 28.2 + - - -
999D MG 4.0 1.0 - - - -
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Residues in contact with ILE 120 (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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41D HIS* 2.9 28.1 + - + +
44D VAL* 3.7 27.8 - - + -
45D CYS* 3.9 18.6 - - - -
48D TYR* 3.4 41.3 - - + -
108D ASP* 2.7 15.9 + - + +
109D LEU* 4.0 16.2 - - + -
118D ILE* 3.9 16.6 - - + -
119D GLU* 1.3 85.8 - - - +
121D GLY* 1.3 69.2 + - - +
122D VAL* 4.6 0.2 - - + -
134D LYS* 4.0 0.7 - - - -
146D HIS* 3.3 10.8 - - + +
148D PHE* 4.4 2.2 - - + -
257D TMP 3.3 1.2 + - - -
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Residues in contact with GLY 121 (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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41D HIS* 4.6 1.6 - - - -
120D ILE* 1.3 73.8 - - - +
122D VAL* 1.3 62.1 + - - +
130D TYR* 3.5 22.9 - - - -
134D LYS* 3.6 5.2 - - - -
146D HIS 2.9 10.9 + - - +
147D ILE* 3.2 11.3 - - - +
148D PHE* 2.8 34.2 + - - +
257D TMP 4.6 0.2 - - - -
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Residues in contact with VAL 122 (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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37D ALA* 5.7 1.4 - - - +
40D THR* 3.7 15.9 - - + -
41D HIS* 4.2 26.6 - - + -
44D VAL* 3.9 35.4 - - + -
120D ILE* 4.6 0.2 - - + -
121D GLY* 1.3 78.8 - - - +
123D THR* 1.3 63.0 + - - +
124D ARG* 5.2 4.3 + - - -
130D TYR* 3.8 13.5 + - - -
148D PHE* 3.3 11.0 - - + +
150D PHE* 3.5 28.4 - - + -
175D LEU* 4.1 10.1 - - + -
195D GLU* 4.4 4.0 - - - +
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Residues in contact with THR 123 (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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121D GLY 4.2 0.2 - - - -
122D VAL* 1.3 74.2 - - - +
124D ARG* 1.3 57.6 + - - +
125D ARG* 2.7 35.1 + - - +
126D GLU 4.0 0.7 - - - +
127D VAL* 3.9 27.1 - - + -
130D TYR* 3.7 17.4 - - + +
147D ILE* 3.9 7.2 - - + -
148D PHE 2.9 15.8 + - - +
149D SER* 3.3 24.7 - - - -
150D PHE* 3.3 13.1 + - - -
195D GLU* 2.6 26.5 + - - -
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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