Contacts of the strand formed by residues 123 - 127 (chain A) in PDB entry 3JPW
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 ILE 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ILE* 5.4 2.2 - - + -
89A MET* 5.8 0.7 - - - -
97A VAL* 3.3 34.8 - - + +
99A PHE* 4.8 0.7 - - + -
112A LEU* 3.7 39.3 - - + +
115A ILE* 4.0 17.7 - - + -
116A SER* 3.9 19.7 - - - +
119A THR* 5.5 0.7 - - - +
121A THR* 3.4 10.7 + - + +
122A PRO* 1.3 79.7 - - - +
124A LEU* 1.3 71.6 + - - +
142A MET 2.9 7.3 + - - -
143A PHE* 3.3 19.4 - - + -
144A PHE 2.9 24.8 + - - -
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Residues in contact with LEU 124 (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 VAL 2.8 16.4 + - - +
98A VAL* 4.7 2.7 - - + -
99A PHE* 2.9 31.9 + - - +
122A PRO* 5.1 2.9 - - + -
123A ILE* 1.3 85.3 - - - +
125A GLY* 1.3 60.2 + - - +
126A ILE* 3.6 13.3 + - + +
144A PHE* 3.4 33.0 - - + +
146A PHE* 4.4 7.2 - - + -
296A GLY* 3.7 35.2 - - - +
299A ILE* 3.9 27.8 - - + -
300A ILE* 4.3 14.4 - - + -
339A LEU* 5.8 1.3 - - + -
351A PHE* 4.7 4.9 - - + -
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Residues in contact with GLY 125 (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 PHE 3.7 1.8 - - - -
112A LEU* 4.8 1.6 - - - -
123A ILE 4.0 0.8 + - - -
124A LEU* 1.3 69.9 - - - +
126A ILE* 1.3 60.4 + - - -
127A HIS 3.5 2.2 - - - -
130A SER* 3.3 31.2 - - - -
131A SER* 3.2 10.4 - - - -
143A PHE* 4.0 6.3 - - - -
144A PHE 2.7 14.9 + - - -
145A GLN* 3.5 0.5 - - - -
146A PHE* 2.9 27.2 + - - -
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Residues in contact with ILE 126 (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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41A LEU* 5.3 0.7 - - + -
98A VAL* 3.7 28.7 - - + -
99A PHE 2.9 16.0 + - - +
100A ALA* 3.6 18.8 - - + -
124A LEU* 3.9 10.3 - - + +
125A GLY* 1.3 76.3 - - - -
127A HIS* 1.3 61.9 + - + +
131A SER* 4.3 0.9 - - - -
146A PHE* 3.7 44.2 - - + +
289A LEU* 4.0 3.8 - - + -
292A ARG* 2.9 33.3 + - + +
293A VAL* 3.7 39.5 - - + +
296A GLY* 5.0 0.4 - - - -
602A CL 4.2 0.3 - - - +
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Residues in contact with HIS 127 (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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44A THR* 5.8 0.2 - - + -
100A ALA* 4.4 6.1 - - + -
101A ASP* 2.9 50.2 + - - +
102A ASP* 3.0 23.0 + - - -
125A GLY 3.5 2.0 + - - -
126A ILE* 1.3 90.9 - - + +
128A GLY* 1.3 65.9 + - - +
130A SER* 3.2 7.0 + - - -
131A SER* 3.6 8.3 - - - -
265A ASP* 6.4 0.2 - - - -
282A TYR 4.5 0.2 + - - -
283A ASP* 2.9 32.1 + - - -
284A GLU* 3.0 41.3 + - + +
289A LEU* 4.7 4.9 - - + -
292A ARG* 3.9 4.4 + - - +
602A CL 3.6 12.8 - - + +
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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