Contacts of the strand formed by residues 144 - 149 (chain B) 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 HIS 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B TYR* 5.6 0.2 - - - -
116B ARG* 3.6 33.5 + - - +
117B PHE 2.9 16.0 + - - +
118B ILE* 3.4 7.9 - - + +
119B GLU* 2.6 32.7 + - - +
142B LYS 3.4 4.0 + - - -
143B THR* 1.3 76.1 - - - +
145B ILE* 1.3 69.1 + - - +
146B HIS* 4.2 3.8 - - + -
156B ALA* 4.7 2.0 - - + -
157B THR* 3.1 37.3 + - + +
158B LYS* 5.0 3.4 - - + -
160B ASP* 2.9 39.4 + - + +
162B THR* 3.8 15.5 - - - -
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLU* 3.4 18.4 - - + +
131B TYR* 3.5 30.4 - - + +
134B LYS* 4.2 12.6 - - + -
135B ALA* 3.6 40.2 - - + +
138B ILE* 6.1 0.9 - - + -
140B SER* 3.6 22.7 - - - +
143B THR 4.4 0.9 - - - +
144B HIS* 1.3 79.8 - - - +
146B HIS* 1.3 62.6 + - - +
147B ILE* 3.4 28.0 - - + -
156B ALA* 3.1 4.7 - - - +
157B THR* 2.7 36.8 + - + +
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Residues in contact with HIS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 2.8 36.8 + + + +
118B ILE* 4.6 4.2 - - + +
119B GLU 2.9 8.7 + - - +
120B ILE* 3.4 13.8 - - + +
121B GLY 3.0 23.2 + - - +
144B HIS* 4.2 2.9 - - + -
145B ILE* 1.3 74.5 - - - +
147B ILE* 1.3 71.2 + - - +
148B PHE* 3.4 23.5 - + - -
154B GLU* 2.8 28.6 + - + -
155B MET 3.7 6.3 - - - -
156B ALA* 4.0 9.6 - - + +
161B TYR* 3.2 32.1 + + - -
162B THR* 4.8 0.6 + - - -
168B ARG* 3.7 9.4 - - + -
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLY* 3.4 19.7 - - - +
123B THR* 4.1 2.0 - - + -
127B VAL* 3.9 31.9 - - + +
130B TYR* 3.9 25.6 - - + -
131B TYR* 3.6 26.7 - - + -
134B LYS* 4.2 6.3 - - + -
145B ILE* 3.4 27.1 - - + -
146B HIS* 1.3 77.5 - - - +
148B PHE* 1.3 69.1 + - - +
154B GLU* 3.1 10.0 - - - +
155B MET* 2.8 42.6 + - + +
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Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 4.1 19.1 - - + -
48B TYR* 3.8 20.6 - + - -
120B ILE* 4.6 2.7 - - + -
121B GLY 3.0 14.9 + - - +
122B VAL* 3.2 5.9 - - + -
123B THR* 2.8 26.2 + - - +
127B VAL* 4.2 3.1 - - - -
146B HIS* 3.4 41.5 - + - -
147B ILE* 1.3 76.3 - - - +
149B SER* 1.3 60.6 + - - +
153B GLU 3.6 3.6 - - - -
154B GLU* 3.8 13.9 - - + -
168B ARG* 4.4 13.9 - - + -
171B ILE* 3.8 36.8 - - + -
172B LYS* 4.4 14.8 - - + -
175B LEU* 3.6 19.1 - - + -
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B THR* 3.2 13.2 - - - -
124B ARG 5.8 0.2 - - - -
125B ARG 4.0 12.8 - - - -
127B VAL* 3.6 18.6 - - - +
148B PHE* 1.3 75.7 - - - +
150B PHE* 1.3 64.5 + - - +
151B THR* 2.7 25.5 + - - -
152B GLY* 3.4 9.4 + - - -
153B GLU* 3.0 24.4 + - - +
172B LYS* 5.2 1.7 - - - +
175B LEU* 3.7 14.9 - - - +
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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