Contacts of the strand formed by residues 121 - 131 (chain B) in PDB entry 5IYB
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 SER 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B PRO* 3.2 18.3 - - - +
97B THR 3.5 11.4 + - - +
108B MET* 4.5 1.6 - - - +
119B THR* 2.8 23.5 + - - +
120B TYR* 1.3 75.0 - - - +
122B ALA* 1.3 60.0 + - - +
151B LYS* 3.9 21.8 - - - +
152B ILE 3.1 26.7 - - - -
153B PRO* 3.6 6.7 - - - -
154B ILE* 3.9 6.7 - - - -
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Residues in contact with ALA 122 (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 LEU* 4.0 9.1 - - + +
94B SER 3.1 28.9 - - - +
96B PRO* 3.5 14.4 - - + -
121B SER* 1.3 74.8 - - - +
123B PRO* 1.4 66.3 - - + +
124B LEU 3.8 0.2 + - - -
151B LYS* 4.3 4.5 - - - -
152B ILE* 2.8 30.3 + - - +
154B ILE* 3.7 18.7 - - + +
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Residues in contact with PRO 123 (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 LEU* 3.7 2.1 - - - +
94B SER* 3.1 36.7 + - - -
95B LYS 4.0 10.3 - - - +
97B THR* 4.0 15.3 - - - +
99B TRP* 3.7 23.8 - - + -
121B SER 4.7 0.2 - - - +
122B ALA* 1.4 88.7 - - + +
124B LEU* 1.3 58.5 + - - +
125B TYR* 3.3 32.8 - - + +
148B PHE* 3.8 14.1 - - + -
150B GLY 3.6 5.8 - - - +
151B LYS* 4.2 6.3 - - + -
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Residues in contact with LEU 124 (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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51B ILE* 5.9 1.8 - - + -
55B VAL* 4.8 6.1 - - + -
91B ILE* 3.8 21.8 - - + -
92B TYR 3.4 12.6 - - - +
93B LEU* 4.1 22.2 - - + -
123B PRO* 1.3 72.2 - - - +
125B TYR* 1.3 64.6 + - - +
148B PHE* 3.6 4.6 - - - -
149B ILE* 3.0 51.2 + - + +
150B GLY 2.8 16.7 + - - +
152B ILE* 4.0 26.0 - - + -
404B PHE* 4.1 24.5 - - + -
440B ILE* 5.0 5.6 - - + -
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Residues in contact with TYR 125 (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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91B ILE* 3.3 6.1 - - - +
92B TYR* 2.5 50.4 + - + +
94B SER* 3.0 25.3 + - - -
99B TRP* 4.6 8.1 - - - -
123B PRO* 3.3 38.2 - - + +
124B LEU* 1.3 74.3 - - - +
126B VAL* 1.3 61.4 + - - +
146B LYS* 4.9 5.6 - - + -
147B THR* 3.0 12.8 - - - +
148B PHE* 3.6 36.3 - + + -
149B ILE* 4.2 1.3 - - - -
145T LEU* 3.3 27.8 - - + -
148T VAL* 3.4 33.8 + - + +
151T THR* 4.4 9.4 - - + -
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Residues in contact with VAL 126 (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* 4.8 7.0 - - + -
88B PHE* 4.0 19.1 - - + -
89B GLU 3.9 11.7 - - - +
90B GLN 3.3 13.5 - - - +
91B ILE* 4.2 8.7 - - + -
92B TYR* 5.1 0.7 - - - -
125B TYR* 1.3 74.7 - - - +
127B ASP* 1.3 71.9 + - - +
128B ILE* 3.5 23.3 + - + +
146B LYS* 3.8 5.2 - - - -
147B THR 2.9 30.5 + - - +
149B ILE* 3.7 35.7 - - + -
408B PHE* 6.3 1.1 - - + -
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Residues in contact with ASP 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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87B LYS 4.2 0.2 - - - +
88B PHE* 3.5 3.3 - - - -
89B GLU* 2.8 47.0 + - + +
90B GLN* 2.8 35.6 + - + +
92B TYR* 4.9 3.5 + - - -
126B VAL* 1.3 72.5 - - - +
128B ILE* 1.3 65.6 + - - +
129B THR* 4.3 4.9 - - - +
144B HIS* 2.5 42.9 + - - -
145B GLN 3.8 4.0 - - - -
146B LYS* 3.7 12.6 + - - +
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Residues in contact with ILE 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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86B LEU* 4.9 7.2 - - + -
87B LYS 3.8 6.7 - - - +
88B PHE* 3.9 25.8 - - + -
126B VAL* 3.5 20.3 + - + +
127B ASP* 1.3 80.1 + - - +
129B THR* 1.3 73.6 + - - +
143B GLN 3.8 2.1 - - - +
145B GLN* 3.6 30.0 + - + +
147B THR* 3.4 31.0 - - + +
431B LEU* 3.6 29.8 - - + -
435B ILE* 3.8 25.6 - - + -
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Residues in contact with THR 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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85B LEU 3.7 0.5 - - - +
86B LEU* 3.4 9.9 - - - +
87B LYS* 3.0 60.6 + - - +
89B GLU* 4.6 10.0 + - - +
127B ASP* 4.3 11.0 - - - +
128B ILE* 1.3 81.9 - - - +
130B LYS* 1.3 59.3 + - - +
131B THR* 4.1 10.8 + - - -
142B THR* 4.4 9.6 - - - +
143B GLN 3.7 14.1 - - - +
144B HIS* 4.8 5.6 - - + -
431B LEU* 5.5 0.7 - - - -
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Residues in contact with LYS 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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84B TYR* 4.7 18.0 - - + -
85B LEU 3.5 3.4 - - - +
86B LEU* 4.0 18.6 - - + -
129B THR* 1.3 72.9 - - - +
131B THR* 1.3 63.2 + - - +
132B VAL* 4.1 11.7 - - + -
141B GLN 3.9 3.6 - - - +
142B THR* 3.3 25.5 + - - -
143B GLN* 3.5 37.0 + - + +
145B GLN* 5.5 10.4 - - - +
429B PHE* 3.5 41.7 + - + +
430B ASN* 6.1 0.4 - - - +
431B LEU* 5.2 11.1 - - + +
159T HIS* 5.8 5.9 - - - -
160T GLN* 6.0 0.4 + - - -
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Residues in contact with THR 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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83B ARG 5.6 0.2 - - - -
84B TYR* 4.4 1.3 - - - -
85B LEU* 3.0 54.1 + - + +
87B LYS* 5.3 7.8 - - - +
129B THR* 4.1 9.7 + - - -
130B LYS* 1.3 82.6 + - - +
132B VAL* 1.3 60.6 + - - +
133B ILE* 3.5 20.5 + - + +
139B GLN 5.4 2.0 - - - +
140B LEU* 5.7 3.8 - - + -
141B GLN 4.5 0.7 - - - -
142B THR* 3.9 19.5 + - - +
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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