Contacts of the strand formed by residues 135 - 146 (chain B) in PDB entry 6IY6
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 VAL 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B LEU* 3.4 31.6 - - + +
52B THR* 4.2 2.5 - - - +
53B ILE* 3.9 24.0 - - + -
56B ALA* 4.8 1.3 - - + -
87B VAL* 4.1 8.0 - - + +
88B GLN* 5.0 1.4 + - - +
120B VAL* 3.6 34.3 - - + -
121B ARG 3.6 11.7 - - - +
122B LYS* 4.1 8.7 - - - +
123B VAL* 3.6 8.8 - - - +
127B ILE* 4.7 3.5 - - - +
132B GLN* 3.2 23.1 - - + +
133B GLN 3.3 1.5 - - - -
134B ASP* 1.3 84.3 - - + +
136B GLU* 1.3 60.9 + - - +
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Residues in contact with GLU 136 (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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77B PHE* 4.1 0.6 - - - -
87B VAL* 4.6 3.8 - - - -
88B GLN* 3.3 40.2 + - + +
90B LEU* 3.5 29.8 - - - +
120B VAL* 3.7 4.4 - - - -
121B ARG* 3.0 38.0 + - + +
122B LYS 5.8 0.4 - - - +
123B VAL* 3.5 16.1 - - + +
127B ILE* 5.5 0.2 - - + -
135B VAL* 1.3 75.6 - - - +
137B LEU* 1.3 59.7 + - - +
138B HIS* 2.9 33.9 + - + -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 5.0 4.9 - - + -
60B VAL* 4.1 17.3 - - + -
62B VAL* 4.4 17.0 - - + -
80B LEU* 3.8 17.9 - - + -
87B VAL* 4.7 13.4 - - + +
88B GLN 2.9 14.6 + - - +
89B ALA* 3.3 6.3 - - + +
90B LEU* 2.8 30.4 + - - -
116B VAL* 3.7 28.3 - - + +
118B GLY* 3.7 34.1 - - - +
119B VAL 3.7 8.1 - - - +
120B VAL* 4.1 6.1 - - + +
136B GLU* 1.3 71.8 - - - +
138B HIS* 1.3 57.6 + - - +
139B VAL* 3.4 1.8 + - - +
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Residues in contact with HIS 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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90B LEU* 3.8 22.5 + - + +
92B ALA* 5.6 7.3 - - + +
96B HIS* 5.2 10.3 + - + +
118B GLY* 3.2 2.0 - - - -
119B VAL* 2.8 45.2 + - + +
121B ARG* 3.2 62.3 + - + +
136B GLU* 2.9 34.2 + - + -
137B LEU* 1.3 66.8 - - - +
139B VAL* 1.3 63.1 - - - +
140B GLN* 4.0 3.5 - - - +
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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
----------------------------------------------------------
78B LEU* 5.1 0.9 - - + -
89B ALA* 4.1 12.6 - - + -
90B LEU 2.9 29.2 + - - +
91B VAL* 3.8 31.1 - - + +
92B ALA 5.5 1.6 + - - -
96B HIS* 4.0 16.1 - - - +
97B ALA* 5.3 3.6 - - - +
101B MET* 4.5 6.3 - - + -
116B VAL* 4.2 14.4 - - + -
118B GLY* 4.1 6.3 - - - -
137B LEU* 3.9 9.0 - - + +
138B HIS* 1.3 73.8 - - - +
140B GLN* 1.3 65.3 + - - +
141B LYS 3.4 26.9 - - - +
142B ILE* 4.4 10.3 - - + -
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Residues in contact with GLN 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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28B ARG* 3.5 23.7 + - - +
59B VAL* 3.9 21.1 - - - +
96B HIS* 4.7 25.4 + - + +
97B ALA* 6.1 0.4 - - - -
101B MET* 3.5 9.9 - - - +
117B GLU* 2.8 28.7 + - - +
118B GLY* 4.4 1.3 - - - +
119B VAL* 3.2 30.0 - - + +
121B ARG* 6.0 0.6 - - - +
138B HIS 4.0 6.7 - - - +
139B VAL* 1.3 76.7 - - - +
141B LYS* 1.3 66.0 + - + +
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Residues in contact with LYS 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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27B GLU 5.9 0.2 - - - -
28B ARG* 3.3 27.6 - - + +
61B TRP* 4.2 14.6 - - + -
101B MET* 3.6 2.7 - - - -
115B ASP 4.5 0.2 - - - -
116B VAL* 3.5 4.0 - - - -
117B GLU* 3.0 55.9 + - + +
139B VAL* 3.4 14.5 - - - +
140B GLN* 1.3 80.0 - - + +
142B ILE* 1.3 61.5 + - - +
143B TYR* 3.6 30.9 + - + +
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Residues in contact with ILE 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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28B ARG 3.2 4.9 + - - -
29B TYR* 3.1 26.7 - - + +
30B GLY 3.6 1.9 + - - -
78B LEU* 3.9 24.9 - - + -
80B LEU* 5.6 0.7 - - + -
91B VAL* 5.0 4.0 - - + -
101B MET* 3.7 20.1 - - + +
104B PHE* 4.2 12.3 - - + -
105B ALA* 4.8 12.8 - - + -
108B ILE* 3.6 27.8 - - + -
114B VAL* 4.2 12.3 - - + -
115B ASP 3.5 4.0 - - - -
116B VAL* 4.1 19.5 - - + -
139B VAL* 4.4 9.2 - - + -
141B LYS* 1.3 73.9 - - - +
143B TYR* 1.3 61.6 + - - +
144B VAL 4.3 0.2 - - - -
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Residues in contact with TYR 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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27B GLU 2.8 27.2 + - - -
28B ARG 3.3 16.6 + - - -
29B TYR 4.6 8.1 - - - -
30B GLY 3.4 12.3 - - - +
32B SER* 4.1 28.3 - - - +
43B ARG* 5.9 2.5 - - - -
61B TRP* 4.4 13.9 - + - -
114B VAL* 3.1 5.3 - - - -
115B ASP* 2.8 50.5 + - + +
141B LYS* 3.6 35.3 + - + +
142B ILE* 1.3 75.5 - - - +
144B VAL* 1.3 60.6 + - - +
145B ILE* 3.4 3.8 + - + +
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Residues in contact with VAL 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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30B GLY 3.2 6.4 + - - +
31B ILE* 3.6 25.1 - - + +
32B SER* 3.3 22.3 + - - +
104B PHE* 3.9 13.5 - - + -
108B ILE* 3.6 40.2 - - + -
112B SER* 4.2 4.0 - - - -
113B ILE 3.6 6.7 - - - +
114B VAL* 3.8 6.7 - - + -
142B ILE 4.3 0.2 - - - -
143B TYR* 1.3 66.4 - - - +
145B ILE* 1.3 60.0 + - - +
146B SER 3.5 8.7 - - - +
147B LEU* 3.5 37.2 - - + +
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Residues in contact with ILE 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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297A TYR* 5.5 0.2 - - + -
433A HIS* 4.8 10.1 + - - +
465A PRO* 3.9 27.1 - - + -
32B SER* 3.6 24.6 - - - +
33B SER 5.2 0.2 - - - +
34B MET* 5.0 6.8 - - - -
35B ILE* 3.9 26.9 - - + +
63B ARG* 4.3 4.0 - - - +
113B ILE* 3.1 34.5 + - + +
115B ASP* 3.4 41.7 - - + +
143B TYR* 3.4 7.1 + - + +
144B VAL* 1.3 73.0 - - - +
146B SER* 1.3 69.4 - - - +
147B LEU 4.2 0.2 - - - -
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Residues in contact with SER 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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433A HIS* 4.9 4.5 + - - -
459A PHE 5.1 0.9 + - - -
462A GLY* 3.7 2.4 + - - -
463A ALA* 2.9 46.9 + - - +
112B SER* 3.3 8.0 - - - -
113B ILE* 2.9 35.0 + - - +
144B VAL* 3.5 3.1 - - - +
145B ILE* 1.3 90.5 - - - +
147B LEU* 1.3 59.9 + - - +
148B ALA 3.5 0.2 + - - -
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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