Contacts of the strand formed by residues 97 - 103 (chain B) in PDB entry 1X8E
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 GLU 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LEU* 3.8 1.6 - - - -
88B HIS* 3.3 15.5 + - - -
90B HIS* 2.4 44.3 + - + -
96B ALA* 1.3 73.7 - - - +
98B VAL* 1.3 68.0 + - - +
99B TYR* 3.2 30.0 + - + -
129B TYR* 3.9 3.5 - - - -
130B VAL* 2.9 39.6 + - + +
136B HIS* 3.6 10.8 - - - -
150B ALA* 4.4 0.3 - - - +
151B ILE 3.5 10.5 - - - +
152B TYR* 3.5 33.0 - - + +
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.9 26.7 - - + +
68A PHE* 4.3 20.6 - - + -
149A LEU* 5.5 0.2 - - + -
151A ILE* 4.5 23.3 - - + -
97B GLU* 1.3 80.4 - - - +
99B TYR* 1.3 67.9 + - - +
100B VAL* 4.6 4.7 - - + -
127B VAL* 3.4 28.0 - - + -
128B VAL 3.3 6.5 - - - +
129B TYR* 4.7 8.1 - - + -
150B ALA* 3.4 1.7 - - - -
151B ILE* 2.9 36.8 + - + +
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Residues in contact with TYR 99 (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 HIS* 3.7 9.9 + - - -
97B GLU* 3.2 25.2 + - + -
98B VAL* 1.3 80.5 - - - +
100B VAL* 1.3 61.7 + - - +
108B MET* 3.7 22.2 - - + -
122B MET* 3.9 17.3 - - + -
126B THR 4.4 0.9 - - - -
127B VAL* 3.0 13.0 - - - +
128B VAL* 2.9 31.4 + - + +
130B VAL* 3.9 6.3 - - + -
136B HIS* 2.5 43.9 + + - -
138B THR* 4.3 12.0 + - + -
148B PHE* 3.5 40.8 - + - -
149B LEU 3.3 4.0 - - - -
150B ALA* 3.9 13.9 - - + +
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Residues in contact with VAL 100 (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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12A PHE* 3.9 19.7 - - + -
100A VAL* 6.2 2.7 - - + -
102A LEU* 6.2 1.3 - - + -
149A LEU* 3.5 32.3 - - + -
98B VAL* 4.6 4.0 - - + -
99B TYR* 1.3 78.5 - - - +
101B ALA* 1.3 63.0 + - - +
102B LEU* 3.6 23.2 + - + +
122B MET* 4.9 0.7 - - - -
125B GLY 5.9 0.4 - - - -
126B THR 3.6 4.9 - - - -
127B VAL* 3.9 15.5 - - + -
148B PHE* 3.5 2.2 - - - +
149B LEU* 2.9 50.3 + - + +
151B ILE* 5.2 3.8 - - + -
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Residues in contact with ALA 101 (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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12A PHE* 4.2 2.4 - - - -
100B VAL* 1.3 75.7 - - - +
102B LEU* 1.3 63.2 + - - +
103B LYS 3.9 0.4 - - - +
122B MET* 4.2 15.5 - - + -
123B GLU 3.5 25.8 - - - +
124B PRO* 3.4 2.7 - - + +
125B GLY 3.2 21.3 + - - -
126B THR* 3.0 18.1 + - - +
146B PHE* 4.2 16.8 - - + -
148B PHE* 4.1 7.0 - - - -
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Residues in contact with LEU 102 (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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12A PHE* 4.0 20.3 - - + -
10B VAL* 4.6 2.9 - - + -
11B ASP 4.8 0.7 - - - +
12B PHE* 3.7 58.9 - - + +
70B THR* 4.4 15.0 - - + -
100B VAL* 3.7 33.0 - - + +
101B ALA* 1.3 75.5 - - - +
103B LYS* 1.3 62.0 + - - +
124B PRO* 3.9 14.7 - - - +
147B ILE* 3.0 21.5 + - + +
148B PHE* 4.2 6.5 - - - -
149B LEU* 4.4 17.3 - - + -
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Residues in contact with LYS 103 (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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12B PHE 4.1 6.7 - - - +
13B GLU* 3.0 56.6 + - - +
101B ALA 3.9 0.4 - - - -
102B LEU* 1.3 78.6 + - - +
104B GLY* 1.3 67.3 + - - +
124B PRO* 4.2 9.5 - - + +
145B PRO* 4.2 5.8 - - + +
146B PHE* 3.5 6.9 - - - -
147B ILE* 3.2 44.4 + - + +
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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