Contacts of the strand formed by residues 141 - 153 (chain B) in PDB entry 5IY8
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 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B LYS 3.7 2.3 - - - +
132B VAL* 2.7 64.8 + - + +
138B GLU* 3.1 27.3 + - + +
139B GLN 3.5 2.5 + - - +
140B LEU* 1.3 74.4 - - - +
142B THR* 1.3 68.2 + - - +
143B GLN* 5.2 6.2 - - - +
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Residues in contact with THR 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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129B THR* 4.0 17.9 - - + -
130B LYS 3.5 10.8 - - - +
131B THR* 4.0 14.6 - - + +
139B GLN 5.3 1.6 + - - -
140B LEU* 3.3 12.9 + - - +
141B GLN* 1.3 80.9 + - - +
143B GLN* 1.3 66.1 + - - +
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Residues in contact with GLN 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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128B ILE 4.1 1.2 - - - +
129B THR* 3.7 10.5 - - - +
130B LYS* 3.2 57.8 + - + +
141B GLN* 5.2 6.6 - - - +
142B THR* 1.3 78.8 - - - +
144B HIS* 1.3 63.0 + - - +
145B GLN* 3.9 28.3 + - - +
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Residues in contact with HIS 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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89B GLU* 3.5 21.8 + - - -
127B ASP* 2.6 38.7 + - + -
128B ILE 4.3 4.3 + - - -
129B THR* 4.7 10.5 + - + +
143B GLN* 1.3 74.2 - - - +
145B GLN* 1.3 82.3 + - - +
146B LYS* 5.4 6.4 + - + -
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Residues in contact with GLN 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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127B ASP* 3.5 26.0 - - - +
128B ILE* 3.4 22.4 + - + +
129B THR* 5.7 0.2 - - - -
130B LYS* 5.4 5.0 - - + -
143B GLN* 3.9 32.5 + - + +
144B HIS* 1.3 101.2 + - - +
146B LYS* 1.3 59.4 + - - +
147B THR* 3.9 13.5 - - - +
431B LEU* 4.4 20.2 - - + +
432B GLU* 3.9 23.6 - - - +
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Residues in contact with LYS 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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92B TYR* 3.1 45.1 + - + -
125B TYR* 4.5 13.4 - - + -
126B VAL 3.9 2.5 - - - -
127B ASP* 3.8 11.2 + - - +
144B HIS* 5.4 5.3 + - + -
145B GLN* 1.3 74.4 - - - +
147B THR* 1.3 60.8 + - - +
148B PHE 4.2 0.3 + - - -
145T LEU* 4.6 19.8 - - + +
150T THR* 4.6 14.1 + - + +
151T THR* 4.9 5.7 - - - +
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Residues in contact with THR 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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125B TYR* 3.1 5.9 - - - -
126B VAL* 2.8 43.0 + - - +
128B ILE* 3.9 27.0 - - + +
145B GLN* 3.9 12.3 - - - +
146B LYS* 1.3 84.0 + - - +
148B PHE* 1.3 74.0 + - - +
149B ILE* 3.6 1.1 + - + -
431B LEU* 5.8 1.7 - - + +
432B GLU* 4.7 29.8 + - + +
435B ILE* 4.9 9.9 - - + -
151T THR* 5.2 7.4 - - + -
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Residues in contact with PHE 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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99B TRP* 5.0 4.9 - + - -
123B PRO* 3.3 35.7 - - + -
124B LEU 3.8 8.7 - - - -
125B TYR* 3.6 25.7 - + + -
147B THR* 1.3 84.9 - - + +
149B ILE* 1.3 59.8 + - - +
150B GLY 3.5 18.4 - - - -
151B LYS* 3.7 35.7 - - + -
435B ILE* 4.2 4.2 - - - +
437B THR* 3.8 28.8 - - + +
126M ASP* 4.8 6.1 - - - -
127M ARG* 6.1 3.6 - - - -
129M ASN* 4.9 9.4 - - - -
151T THR* 5.0 10.8 - - + +
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Residues in contact with ILE 149 (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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59B VAL* 5.7 1.3 - - + -
88B PHE* 6.1 0.9 - - + -
91B ILE* 5.3 1.6 - - + -
124B LEU* 3.1 42.1 + - + +
126B VAL* 3.6 38.1 - - + -
128B ILE* 5.1 1.6 - - + -
147B THR 4.2 1.8 - - - +
148B PHE* 1.3 76.7 - - - +
150B GLY* 1.3 62.6 + - - +
404B PHE* 5.1 1.1 - - + -
408B PHE* 4.5 16.8 - - + -
411B LEU* 4.7 4.1 - - + +
435B ILE* 4.0 31.1 - - + +
437B THR* 3.3 27.6 - - - +
440B ILE* 4.0 25.7 - - + +
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Residues in contact with GLY 150 (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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124B LEU* 2.9 30.4 + - - +
148B PHE* 3.5 13.5 - - - -
149B ILE* 1.3 84.6 - - - +
151B LYS* 1.3 63.5 + - - -
437B THR 4.1 1.3 - - - -
440B ILE* 4.4 11.4 - - - -
441B SER* 3.2 15.7 - - - -
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Residues in contact with LYS 151 (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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99B TRP* 4.1 21.2 - - + -
121B SER* 3.7 21.6 - - - +
122B ALA 3.6 4.0 - - - +
123B PRO* 4.3 9.9 - - + -
148B PHE* 3.7 26.6 - - + -
150B GLY* 1.3 74.1 - - - +
152B ILE* 1.3 67.5 + - - +
153B PRO* 3.6 6.9 - - - +
440B ILE* 4.5 2.5 - - - +
441B SER* 3.3 43.0 + - - +
444B LEU* 4.8 0.5 - - - +
126M ASP* 3.7 29.0 + - - -
129M ASN* 4.0 13.7 + - - -
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Residues in contact with ILE 152 (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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47B PHE* 4.8 2.9 - - + -
50B PHE* 4.7 9.4 - - + -
51B ILE* 4.3 22.2 - - + -
55B VAL* 5.8 0.9 - - + -
93B LEU* 4.7 6.7 - - + -
121B SER* 3.5 1.3 - - - -
122B ALA 2.6 41.6 + - - +
124B LEU* 3.8 32.5 - - + -
151B LYS* 1.3 76.5 - - - +
153B PRO* 1.3 78.5 - - + +
154B ILE* 3.3 5.9 + - + +
404B PHE* 3.8 27.1 - - + -
440B ILE* 4.2 9.2 - - + -
444B LEU* 3.7 22.2 - - + -
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Residues in contact with PRO 153 (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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47B PHE* 3.2 21.0 - - + -
119B THR* 5.1 1.6 - - + -
120B TYR 4.0 1.3 - - - +
121B SER* 3.4 14.5 - - - -
151B LYS 3.6 7.4 - - - +
152B ILE* 1.3 90.4 - - + +
154B ILE* 1.3 65.2 + - - +
185B PHE* 3.9 5.0 - - + -
187B ILE* 4.3 16.8 - - + -
400B LEU* 5.4 3.6 - - + -
441B SER 5.7 0.2 - - - +
444B LEU* 3.7 27.8 - - + +
445B LYS* 5.3 2.7 - - - +
448B LEU* 3.8 30.7 - - + -
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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