Contacts of the strand formed by residues 136 - 142 (chain A) in PDB entry 3PHM
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 ASN 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A PHE* 4.1 0.9 - - - -
113A GLY 2.8 40.8 + - - +
114A CYS* 5.2 1.0 - - - +
134A LYS* 3.7 18.9 + - - +
135A ALA* 1.3 71.7 - - - +
137A ILE* 1.3 67.0 + - - +
138A LEU* 3.4 4.0 + - + +
164A SER* 4.4 1.6 + - - -
204A MET* 5.9 4.9 - - + +
331A PHE* 3.2 47.3 - - + +
702A GOL 3.5 25.4 + - - +
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.4 14.1 - - + -
111A LEU 3.7 11.4 - - - +
112A PHE* 3.7 22.0 - - + -
135A ALA 3.5 5.6 + - - +
136A ASN* 1.3 73.5 - - - +
138A LEU* 1.3 66.3 + - - +
139A TYR 4.1 10.5 - - - +
156A PHE* 4.3 2.6 - - - -
204A MET* 3.6 40.2 - - + +
240A ARG* 3.7 30.7 - - - +
274A PHE* 4.0 17.5 - - + -
318A TYR* 3.7 27.8 - - + -
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL* 5.1 3.6 - - + -
97A PHE* 3.7 18.3 - - + -
111A LEU* 2.9 14.6 + - + +
112A PHE 4.1 2.2 - - - -
113A GLY* 3.9 11.7 - - - +
136A ASN* 3.5 16.4 - - + +
137A ILE* 1.3 78.4 - - - +
139A TYR* 1.3 55.6 + - + +
156A PHE* 3.6 35.8 - - + -
158A VAL* 5.0 4.3 - - + -
167A PHE* 3.6 36.3 - - + -
274A PHE* 5.0 0.2 - - - -
320A MET* 3.8 5.3 - - - +
701A GOL 2.7 24.8 + - - -
702A GOL 3.6 31.9 - - - +
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Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE* 3.6 43.7 - + + -
99A PRO* 3.3 33.7 - - + +
109A MET 5.0 1.3 - - - -
110A LEU* 3.3 4.6 - - - +
111A LEU* 2.8 40.3 + - + +
137A ILE* 3.8 6.2 - - - +
138A LEU* 1.3 81.8 - - - +
140A ALA* 1.3 73.8 + - - +
141A TRP* 3.6 18.7 - - + -
147A PRO* 3.6 24.7 - - + +
189A VAL* 3.7 36.3 - - + -
274A PHE* 4.6 2.2 - - - -
701A GOL 3.5 19.3 - - - -
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Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A MET 3.2 5.2 - - - -
110A LEU* 3.6 19.7 - - + -
137A ILE* 4.7 0.2 - - + -
139A TYR* 1.3 89.1 - - - +
141A TRP* 1.3 60.4 + - - +
142A ALA 4.2 0.8 + - - -
147A PRO* 4.1 10.2 - - - +
240A ARG* 3.9 16.4 - - - +
272A GLN 4.1 7.4 - - - +
273A ALA* 4.5 2.3 - - - +
274A PHE* 3.8 33.6 + - + +
701A GOL 4.6 0.4 + - - -
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Residues in contact with TRP 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PRO* 3.4 26.4 - - + +
101A ALA* 3.8 18.6 - - + -
102A SER 5.2 1.1 - - - -
103A MET* 4.1 23.1 - - - -
106A VAL* 3.6 34.5 - - + -
107A HIS 4.2 1.1 - - - -
108A HIS* 3.1 8.5 - - - +
109A MET* 2.7 70.4 + - + +
110A LEU* 5.5 0.2 - - - +
139A TYR* 3.6 22.2 - - + -
140A ALA* 1.3 74.1 - - - +
142A ALA* 1.3 65.0 + - - +
143A ARG* 3.7 32.8 - - + -
146A PRO* 5.5 1.0 - - - +
147A PRO* 3.7 22.2 - - + +
272A GLN 5.7 0.4 - - - -
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A HIS 4.0 4.3 - - - +
108A HIS* 4.4 4.9 - - + -
140A ALA 4.2 1.0 - - - -
141A TRP* 1.3 86.3 + - - +
143A ARG* 1.3 68.1 + - - +
144A ASN 3.4 0.3 + - - -
145A ALA 3.5 18.9 + - - +
146A PRO* 4.4 0.9 - - - +
147A PRO* 5.2 0.2 - - - +
271A PRO* 3.5 30.5 - - + -
272A GLN 4.2 3.6 - - - +
273A ALA* 3.7 27.0 - - + +
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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