Contacts of the strand formed by residues 134 - 142 (chain B) in PDB entry 3B94
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 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B GLN* 3.4 6.4 - - - +
101B VAL* 3.2 35.3 + - + +
103B PRO* 4.5 2.4 - - - +
113B PHE* 4.4 7.1 - - - -
127B LEU* 3.3 41.8 - - + +
128B THR 4.7 0.2 - - - +
129B ASN* 3.6 32.4 + - - +
130B LYS* 4.2 19.5 - - - +
132B LYS 3.6 14.8 - - - +
133B ILE* 1.3 75.1 - - - +
135B ASN* 1.3 65.2 + - - +
136B VAL* 4.1 0.9 - - - +
124C ILE* 4.8 4.0 - - - +
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Residues in contact with ASN 135 (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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97B ILE 5.5 0.6 + - - -
98B TYR* 5.3 0.4 - - - +
99B GLY 3.2 14.4 - - - +
100B GLN* 4.7 0.4 - - - +
125B GLN* 3.1 18.7 + - - -
127B LEU* 3.8 6.8 - - - +
134B GLN* 1.3 75.8 - - - +
136B VAL* 1.3 73.9 + - - +
137B GLY 5.3 4.2 - - - -
138B GLY 5.4 0.8 - - - +
124C ILE* 4.9 5.4 + - - +
137C GLY 4.7 2.0 + - - +
138C GLY* 3.7 8.9 - - - -
139C THR* 3.2 38.5 + - - +
140C TYR* 3.4 32.5 - - + +
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 3.6 4.5 - - + +
98B TYR* 3.0 26.9 - - - -
99B GLY* 2.7 13.6 + - - -
100B GLN* 3.3 28.0 - - - +
101B VAL* 3.7 24.5 - - + -
117B LEU* 4.5 8.7 - - + -
125B GLN* 3.4 11.0 - - - +
127B LEU* 4.5 4.9 - - + -
134B GLN 4.1 0.2 - - - +
135B ASN* 1.3 85.6 + - - +
137B GLY* 1.3 61.3 + - - +
150B LEU* 4.3 17.0 - - + -
164B TYR 4.4 2.0 - - - +
165B TRP* 3.8 25.8 - - + -
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Residues in contact with GLY 137 (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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135A ASN* 5.7 0.7 - - - +
97B ILE* 3.3 22.2 - - - -
117B LEU* 4.8 4.5 - - - -
125B GLN* 2.9 25.5 + - - +
135B ASN* 5.3 3.1 - - - -
136B VAL* 1.3 74.8 - - - +
138B GLY* 1.3 59.7 + - - -
140B TYR* 3.7 16.7 + - - -
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Residues in contact with GLY 138 (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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135A ASN* 5.1 3.6 - - - -
96B LEU* 4.7 3.8 - - - -
97B ILE 2.7 33.6 + - - -
135B ASN* 5.4 2.0 - - - +
137B GLY* 1.3 76.7 - - - -
139B THR* 1.3 63.1 + - - -
140B TYR* 3.2 16.0 - - - -
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Residues in contact with THR 139 (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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96A LEU* 3.4 19.3 - - + +
97A ILE 5.2 0.4 - - - -
98A TYR* 3.3 40.2 - - + +
99A GLY 4.7 2.8 + - - +
135A ASN* 3.3 20.6 + - - +
94B LEU* 3.7 18.8 - - + -
95B TYR 3.6 7.0 + - - +
96B LEU* 3.4 25.0 - - - +
138B GLY* 1.3 69.0 - - - -
140B TYR* 1.3 76.2 + - - +
170B LEU* 4.7 1.1 - - + +
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Residues in contact with TYR 140 (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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98A TYR* 5.4 1.8 - - - -
100A GLN* 4.2 20.9 - - - -
135A ASN* 2.6 29.2 + - + +
164A TYR* 5.1 2.0 - - - -
94B LEU* 3.6 5.5 - - - +
95B TYR* 2.6 42.6 + - - +
97B ILE* 4.0 19.5 - - + -
119B LYS* 5.8 4.0 - - + -
124B ILE* 3.7 51.4 + - + +
125B GLN* 4.9 3.3 - - - +
137B GLY* 3.7 14.6 + - - -
138B GLY* 3.2 30.1 - - - -
139B THR* 1.3 88.5 - - - +
141B GLU* 1.3 60.4 + - - +
142B LEU* 3.6 24.6 + - + -
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Residues in contact with GLU 141 (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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61A LYS* 2.9 50.8 + - - +
98A TYR* 3.4 25.5 + - + +
164A TYR* 3.6 28.2 + - + +
93B GLY 3.4 8.7 - - - +
94B LEU* 4.2 9.1 - - + +
119B LYS* 4.8 8.8 + - - +
140B TYR* 1.3 73.7 - - - +
142B LEU* 1.3 70.4 + - - +
143B HIS* 4.7 21.4 + - + +
175B PHE* 4.7 9.7 - - - +
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Residues in contact with LEU 142 (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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89B ILE* 3.9 25.8 - - + -
92B ASN* 3.2 5.4 - - - -
93B GLY 2.9 31.4 + - - +
95B TYR* 3.7 37.7 - - + -
97B ILE* 4.6 7.6 - - + -
119B LYS* 3.9 24.2 - - + -
124B ILE* 6.5 0.4 - - + -
140B TYR* 3.7 18.8 - - + +
141B GLU* 1.3 85.9 - - - +
143B HIS* 1.3 66.7 + - - +
146B ASP* 3.5 7.2 - - - +
148B ILE* 4.1 20.4 - - + -
167B ILE* 4.1 7.2 - - + -
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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