Contacts of the strand formed by residues 147 - 154 (chain B) in PDB entry 3H44
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 THR 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU 3.9 1.2 - - - +
91B ASP* 3.3 3.1 - - - -
92B VAL* 2.7 43.6 + - - +
94B ILE* 2.7 21.9 + - - +
95B GLY* 4.0 1.0 - - - -
107B SER* 4.8 4.5 - - - +
111B GLN* 4.1 5.8 - - + -
141B PHE 3.5 4.9 - - - +
142B THR* 3.9 27.4 - - + +
146B HIS* 1.3 76.1 + - - +
148B ASN* 1.3 60.4 + - - +
149B TYR* 3.3 31.8 - - + +
249B TYR* 3.3 20.1 + - - +
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Residues in contact with ASN 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 4.3 0.6 - - - +
90B LEU 3.5 6.1 - - - -
91B ASP* 3.0 25.1 - - - +
140B ALA* 3.1 8.8 - - - +
141B PHE* 3.0 59.1 + - + -
147B THR* 1.3 73.5 - - - +
149B TYR* 1.3 69.1 + - - +
150B TYR* 3.2 15.6 - - - -
435B SER* 2.7 47.6 + - - +
438B ALA* 4.6 0.3 - - - +
439B GLY* 4.3 1.7 + - - -
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Residues in contact with TYR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 3.0 5.7 - - - +
90B LEU 2.9 39.7 + - - +
92B VAL* 4.7 1.3 - - + -
110B LEU* 3.9 0.2 - - - +
111B GLN* 3.3 37.0 - - + -
114B LEU* 3.6 25.2 - - + +
115B PHE* 4.1 13.5 - + + -
139B ASN 3.8 3.6 - - - -
140B ALA* 4.0 10.5 - - + -
147B THR* 3.3 32.8 - - + +
148B ASN* 1.3 76.7 - - - +
150B TYR* 1.3 62.3 + - - +
165B PHE* 3.7 20.9 - - + -
168B PHE* 4.3 10.1 - + + -
169B PHE* 4.0 14.8 - + + -
249B TYR* 2.7 32.1 + + - -
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Residues in contact with TYR 150 (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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88B ALA 3.4 6.7 - - - +
89B ALA* 3.6 15.5 - - + -
115B PHE* 5.8 0.4 - - - -
138B SER* 2.8 24.0 + - - -
139B ASN* 3.0 58.3 + - + +
140B ALA* 3.9 10.2 + - - -
141B PHE* 4.1 10.5 - + - -
148B ASN* 3.2 23.8 - - - -
149B TYR* 1.3 75.1 - - - +
151B PHE* 1.3 58.1 + - - +
165B PHE* 4.2 4.1 - - - -
431B ARG* 3.6 46.2 + - + +
434B THR* 4.8 0.4 - - - +
435B SER* 3.5 16.6 - - - -
19D ARG* 4.2 18.5 + - - -
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Residues in contact with PHE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B SER 5.2 0.2 - - - -
87B SER* 2.8 34.5 + - - -
88B ALA* 3.1 45.4 + - + +
127B TYR* 3.4 25.6 - + - +
131B LEU* 3.9 14.6 - - + -
137B SER 3.2 14.4 - - - +
138B SER* 3.8 3.8 - - - +
150B TYR* 1.3 74.7 - - - +
152B ASP* 1.3 67.6 + - - +
153B VAL* 3.8 13.0 - - + -
158B LEU* 4.8 5.8 - - + -
161B ALA* 3.5 16.8 - - + -
162B LEU* 3.9 24.0 - - + -
165B PHE* 3.7 25.6 - + + -
431B ARG* 4.2 8.6 - - - +
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Residues in contact with ASP 152 (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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85B LYS* 4.2 30.3 + - + +
86B SER 3.3 13.9 - - - +
87B SER* 3.6 7.9 - - - -
131B LEU* 3.7 5.0 - - - +
135B ALA 4.6 1.0 - - - +
136B GLY* 2.6 29.2 - - - -
137B SER* 2.9 32.2 + - - +
151B PHE* 1.3 76.2 - - - +
153B VAL* 1.3 58.9 + - - +
430B PRO* 5.5 2.1 - - - +
431B ARG* 3.5 28.2 + - + +
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Residues in contact with VAL 153 (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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85B LYS* 3.3 7.8 - - - +
86B SER* 2.8 37.6 + - - +
130B PHE* 4.6 1.6 - - + -
131B LEU* 4.0 21.5 - - + -
134B HIS* 3.4 28.3 - - + +
135B ALA 4.4 0.4 - - - -
136B GLY* 3.5 7.9 - - - +
151B PHE* 3.8 18.8 - - + -
152B ASP* 1.3 77.5 - - - +
154B SER* 1.3 73.8 + - - +
157B HIS* 3.7 24.9 - - + +
158B LEU* 4.0 6.5 - - - -
161B ALA* 4.0 2.0 - - + -
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Residues in contact with SER 154 (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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84B ASP 3.8 9.1 + - - -
85B LYS* 4.6 0.6 - - - +
134B HIS* 2.9 25.8 + - - -
135B ALA* 4.1 6.9 + - - -
153B VAL* 1.3 73.0 - - - +
155B HIS* 1.3 54.3 + - - +
156B GLU* 3.0 15.5 + - - -
157B HIS* 2.9 42.5 + - - +
891B ILE* 3.0 37.4 - - - +
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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