Contacts of the strand formed by residues 116 - 120 (chain A) in PDB entry 3PHW
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 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 3.8 30.3 - - + -
105A ALA* 3.5 44.0 - - + +
108A LEU* 4.1 7.2 - - + -
109A ALA* 3.9 9.6 - - + +
114A ILE* 3.6 25.6 - - + -
115A THR* 1.3 77.4 - - - +
117A ILE* 1.3 70.7 + - - +
118A ILE* 4.4 9.6 - - + -
132A LYS* 3.5 1.4 - - - -
133A PHE* 2.8 40.1 + - + +
142A VAL* 3.4 12.1 - - + +
144A LEU* 4.8 5.8 - - + -
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 4.0 18.4 - - + -
116A ILE* 1.3 77.9 - - - +
118A ILE* 1.3 62.5 + - - +
119A TRP* 3.2 35.8 - - + +
131A ILE 3.5 5.2 - - - +
132A LYS* 3.7 30.7 - - + -
138A VAL* 3.6 35.0 - - + -
141A ALA* 3.7 12.1 - - + -
142A VAL 2.9 7.7 + - - +
143A ASN* 3.5 14.0 - - - +
144A LEU* 2.7 34.5 + - - +
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Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 4.6 4.9 - - + -
102A THR* 3.8 26.9 - - + -
105A ALA* 4.1 13.9 - - + -
116A ILE* 4.4 9.4 - - + -
117A ILE* 1.3 76.9 - - - +
119A TRP* 1.3 64.5 + - - +
120A THR* 3.7 2.1 + - - -
129A ALA 3.9 0.2 - - - +
130A GLY* 3.4 2.3 - - - -
131A ILE* 2.9 39.5 + - + +
133A PHE* 4.0 14.4 - - + -
144A LEU* 3.7 12.3 - - + +
146A HIS* 3.9 25.8 - - + -
152A PHE* 4.0 21.5 - - + -
73B LEU* 4.2 17.7 - - + -
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Residues in contact with TRP 119 (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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4A LEU* 6.0 0.7 - - + -
7A LEU* 4.1 18.4 - - + -
9A TRP* 3.8 22.4 - + - -
19A SER* 3.8 4.9 - - - -
21A PRO* 3.7 26.0 - - + -
23A PHE* 4.1 16.8 - + - -
25A ILE* 4.3 18.2 - - + -
29A PHE* 4.3 8.0 - + - -
117A ILE* 3.2 22.2 - - + +
118A ILE* 1.3 69.4 - - - +
120A THR* 1.3 58.7 + - - +
127A VAL* 3.7 18.2 - - + -
129A ALA 3.7 3.1 - - - -
130A GLY* 3.6 26.2 - - - -
138A VAL* 4.5 5.4 - - + -
143A ASN* 2.9 28.5 + - + -
144A LEU 2.8 20.8 + - - +
145A LEU* 3.5 7.5 - - - +
146A HIS* 2.8 28.4 + - - +
155A LEU* 3.7 18.4 - - + -
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Residues in contact with THR 120 (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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118A ILE 3.7 2.7 + - - +
119A TRP* 1.3 72.2 - - - +
121A VAL* 1.3 63.0 + - - +
127A VAL* 4.0 0.9 - - - -
128A GLU* 3.0 31.4 + - + +
129A ALA* 3.2 27.0 + - + +
131A ILE* 6.0 0.9 - - + -
146A HIS* 3.1 35.4 + - - -
149A GLN* 4.2 11.8 + - - +
8B LEU* 4.4 16.6 - - + -
9B THR* 6.5 0.2 - - + -
73B LEU* 4.2 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
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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