Contacts of the strand formed by residues 126 - 133 (chain B) in PDB entry 4HXD
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 GLN 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B THR* 3.8 24.2 - - + +
23B PHE* 3.4 17.8 - - - +
24B CYS* 4.4 9.6 - - + +
121B VAL* 3.3 5.4 - - - +
122B ASN* 2.6 48.1 + - + +
124B THR* 3.1 25.3 - - + +
125B GLU* 1.3 77.6 - - - +
127B VAL* 1.3 65.6 + - - +
128B THR 3.7 0.5 + - - -
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Residues in contact with VAL 127 (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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21B PRO* 3.9 4.7 - - + -
22B THR* 3.2 27.4 - - - +
23B PHE* 2.9 59.0 + - + +
25B VAL* 4.2 10.8 - - + +
119B TRP* 3.7 27.6 - - + -
120B VAL 3.3 10.1 - - - +
121B VAL* 3.9 4.6 - - + +
126B GLN* 1.3 74.6 - - - +
128B THR* 1.3 62.1 + - - +
129B ALA 3.4 24.7 - - - +
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Residues in contact with THR 128 (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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9A THR* 3.2 34.5 + - + +
102A SO4 4.8 1.2 + - - -
20B ASN* 3.5 16.3 - - - +
21B PRO 3.1 20.4 - - - +
22B THR* 4.4 6.8 + - - -
120B VAL* 3.1 22.8 + - + +
121B VAL 4.7 0.7 - - - -
122B ASN* 4.0 27.1 - - - +
126B GLN 4.5 0.7 - - - +
127B VAL* 1.3 75.2 - - - +
129B ALA* 1.3 64.1 + - - +
149B ARG* 6.4 0.2 - - - +
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Residues in contact with ALA 129 (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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8A LEU* 3.4 40.2 - - + +
9A THR* 4.2 6.7 - - + +
19B THR 3.4 8.5 - - - -
20B ASN* 4.2 0.4 - - - +
21B PRO* 4.7 1.1 - - - -
120B VAL* 3.0 35.9 + - + -
127B VAL* 3.4 11.8 - - - +
128B THR* 1.3 84.2 - - - +
130B ALA* 1.3 62.9 - - - +
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Residues in contact with ALA 130 (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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8A LEU* 4.4 1.7 - - - +
9B TRP* 3.5 25.1 - - + -
18B ILE* 3.3 7.6 - - - +
19B THR* 2.8 37.7 + - + -
21B PRO* 5.3 0.2 - - + -
117B ILE* 4.2 1.3 - - + -
118B LEU 3.3 10.1 - - - +
119B TRP* 3.6 24.2 - - + -
120B VAL* 5.2 0.2 - - - -
127B VAL* 5.1 0.2 - - + -
129B ALA* 1.3 77.7 - - - +
131B ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 131 (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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8A LEU* 3.9 24.7 - - + -
42A ARG* 5.8 1.8 - - - +
70A VAL* 4.5 15.3 - - + -
71A LEU 4.8 0.7 - - - +
73A LEU* 3.5 34.3 - - + -
16B GLN* 5.1 6.5 - - + +
17B TYR 3.3 16.2 - - - +
18B ILE* 4.1 9.0 - - + -
102B SER* 5.0 4.0 - - - -
116B ILE 3.8 0.9 - - - +
117B ILE* 3.2 6.2 - - - -
118B LEU* 2.8 40.7 + - + +
120B VAL* 5.5 0.4 - - + -
130B ALA* 1.3 77.5 - - - +
132B LYS* 1.3 63.1 + - - +
133B PHE* 4.0 33.6 - - + -
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Residues in contact with LYS 132 (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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9B TRP* 3.5 51.0 - - + +
15B GLU 3.8 0.5 - - - +
16B GLN* 3.5 5.0 - - - -
17B TYR* 2.9 54.5 + - + +
115B THR* 4.6 4.0 - - - +
116B ILE 3.6 2.7 - - - -
117B ILE* 3.7 26.5 - - + -
131B ILE* 1.3 74.5 - - - +
133B PHE* 1.3 65.0 + - - +
134B GLY 2.8 28.5 + - - +
135B PRO* 3.5 10.7 + - - +
136B GLY 3.2 27.0 + - - +
138B VAL* 5.3 0.9 - - + -
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Residues in contact with PHE 133 (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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42A ARG* 5.1 3.6 - - - -
15B GLU 4.0 1.6 - - - -
16B GLN* 3.7 33.0 - - + -
78B GLU* 5.3 0.9 - - - -
102B SER* 3.5 25.1 - - - -
105B ALA* 3.5 27.1 - - + +
106B SER* 3.6 28.9 - - - -
109B SER* 3.5 24.7 - - - +
115B THR* 3.1 7.0 - - - -
116B ILE 2.7 46.3 + - - +
118B LEU* 4.0 18.6 - - + -
131B ILE* 4.0 25.6 - - + -
132B LYS* 1.3 73.3 - - - +
134B GLY* 1.3 60.1 + - - +
113D GLN* 4.6 0.4 - - - -
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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