Contacts of the strand formed by residues 136 - 148 (chain B) in PDB entry 1Q4U
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 LEU 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B PHE* 3.8 40.3 - - + +
102B ARG* 4.3 7.1 + - - +
128B SER* 3.8 26.7 - - - +
129B LEU 3.9 5.6 - - - +
130B ARG* 3.6 29.4 - - + +
135B ARG* 1.3 71.9 - - - +
137B CYS* 1.3 60.6 + - - +
138B ALA 3.8 17.7 - - - +
139B VAL* 3.9 10.8 - - + -
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Residues in contact with CYS 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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68B TYR* 4.3 10.2 - - + -
100B PHE* 3.8 1.9 - - - +
101B PHE* 2.8 24.9 + - - -
102B ARG* 3.1 41.7 + - - +
104B VAL* 3.6 26.7 - - + -
109B VAL* 6.4 0.2 - - + -
129B LEU 2.7 17.6 + - - +
130B ARG* 4.9 0.4 - - - -
131B ASP* 3.6 28.9 - - - -
135B ARG 3.2 10.3 + - - -
136B LEU* 1.3 74.9 - - - +
138B ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 4.0 25.8 - - + -
98B THR* 4.4 3.6 - - + -
99B SER 3.2 15.0 - - - +
100B PHE* 4.1 14.1 - - + -
101B PHE* 4.2 5.8 - - - -
129B LEU* 2.8 36.5 + - + +
136B LEU* 3.6 2.8 - - - +
137B CYS* 1.3 82.4 - - - +
139B VAL* 1.3 67.9 + - - +
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Residues in contact with VAL 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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97B HIS 3.8 1.4 - - - +
98B THR* 3.2 5.0 - - - +
99B SER* 2.9 40.1 + - - +
101B PHE* 3.7 32.1 - - + -
127B VAL 3.3 13.0 - - - +
128B SER* 4.5 5.8 - - - +
129B LEU* 4.1 3.8 - - - -
136B LEU* 3.9 18.4 - - + -
138B ALA* 1.3 79.3 - - - +
140B SER* 1.3 62.6 + - - +
141B SER* 6.1 0.9 - - - +
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Residues in contact with SER 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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72B ALA* 3.5 23.2 - - - +
96B ASN* 3.1 22.5 + - - -
97B HIS 3.3 4.0 - - - -
98B THR* 3.3 13.9 + - - -
125B TRP 3.6 1.2 - - - +
126B ASP* 3.7 1.4 - - - -
127B VAL* 2.7 41.5 + - - +
129B LEU* 4.3 2.7 - - - +
139B VAL* 1.3 77.3 - - - +
141B SER* 1.3 62.4 + - - +
142B MET* 3.4 16.2 + - - -
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER* 3.6 5.2 + - - +
96B ASN* 3.8 0.2 - - - -
97B HIS* 2.9 47.0 + - - +
124B PHE* 3.6 27.6 - - - -
125B TRP 3.7 4.7 - - - -
126B ASP* 4.2 7.0 + - - -
139B VAL* 6.1 0.9 - - - +
140B SER* 1.3 70.1 + - - +
142B MET* 1.3 60.5 + - - +
143B SER* 3.9 0.7 + - - -
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Residues in contact with MET 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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72B ALA 3.8 6.5 - - - +
73B GLU* 3.4 41.5 - - + +
76B ALA* 3.5 28.5 - - + -
77B THR* 4.7 0.2 - - - +
93B GLY* 4.8 3.6 - - - -
95B SER 3.7 11.0 - - - +
96B ASN* 3.3 31.2 - - + -
123B TRP 3.8 0.9 - - - +
124B PHE* 3.4 7.5 - - - -
125B TRP* 2.9 39.3 + - + +
127B VAL* 3.9 9.6 - - + -
140B SER* 3.4 15.5 - - - +
141B SER* 1.3 71.9 - - - +
143B SER* 1.3 60.0 + - - +
144B ILE* 3.9 19.5 + - + +
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Residues in contact with SER 143 (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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93B GLY 3.7 0.2 - - - -
94B GLN* 2.8 32.9 + - - +
95B SER* 2.9 33.2 + - - +
122B THR* 3.6 20.4 - - - +
123B TRP 3.7 3.1 - - - -
124B PHE* 4.0 19.0 - - - -
141B SER 3.9 0.9 + - - -
142B MET* 1.3 71.8 - - - +
144B ILE* 1.3 61.6 + - - +
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Residues in contact with ILE 144 (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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76B ALA* 4.0 10.3 - - + +
77B THR* 3.7 23.1 - - - +
80B THR* 3.8 26.5 - - + +
91B ALA* 3.9 14.6 - - + -
92B VAL 3.5 18.6 - - - +
93B GLY* 4.1 3.6 - - - -
94B GLN* 5.0 0.4 - - - -
122B THR* 3.3 6.9 - - - -
123B TRP* 2.8 48.1 + - + +
125B TRP* 3.9 12.6 - - + -
142B MET* 3.9 22.0 - - + +
143B SER* 1.3 80.3 + - - +
145B ALA* 1.3 71.0 + - - +
146B VAL* 3.7 1.4 + - - +
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Residues in contact with ALA 145 (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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371A 4CA 3.9 22.2 - - + -
90B MET* 3.7 2.0 - - - +
91B ALA* 3.2 5.9 - - - -
92B VAL* 2.7 44.0 + - + +
94B GLN* 3.8 24.5 - - + +
121B THR 3.6 6.1 - - - -
122B THR* 4.7 0.2 - - - +
143B SER 4.0 1.6 + - - -
144B ILE* 1.3 73.0 - - - +
146B VAL* 1.3 59.9 - - - +
147B ARG* 3.8 15.9 - - + +
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Residues in contact with VAL 146 (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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80B THR* 3.9 28.3 - - + -
84B VAL* 4.4 10.3 - - + -
89B MET* 3.7 36.4 - - + +
90B MET 3.3 5.2 - - - +
91B ALA* 4.5 1.1 - - + -
120B SER 4.1 9.5 - - - +
121B THR* 2.9 24.4 + - - +
123B TRP* 3.9 21.5 - - + +
144B ILE 4.1 4.5 - - - +
145B ALA* 1.3 77.6 - - - +
147B ARG* 1.3 78.7 + - - +
148B PRO* 4.8 0.2 - - - +
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Residues in contact with ARG 147 (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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371A 4CA 3.5 59.4 + - + +
89B MET* 3.1 7.9 - - - -
90B MET* 2.6 58.9 + - + +
94B GLN* 4.3 10.1 + - - +
121B THR* 2.8 42.9 + - - -
122B THR* 5.6 1.0 + - - -
145B ALA* 3.8 10.6 - - + +
146B VAL* 1.3 86.3 + - - +
148B PRO* 1.3 73.9 - - + +
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Residues in contact with PRO 148 (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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371A 4CA 3.1 21.6 + - - +
88B GLY 3.6 1.8 - - - +
89B MET* 3.5 24.2 - - + -
90B MET* 4.6 0.2 - - - -
146B VAL 4.8 0.2 - - - +
147B ARG* 1.3 93.2 - - + +
149B ARG* 1.3 70.4 + - - +
150B ARG* 4.5 1.4 - - - +
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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