Contacts of the strand formed by residues 147 - 155 (chain D) in PDB entry 2IB8
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 147 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D ILE* 4.1 21.5 - - + -
85D GLU* 3.4 31.4 - - - +
86D VAL* 4.0 11.7 - - + -
87D LYS* 3.0 31.0 + - - +
140D LEU* 4.3 0.4 - - - -
145D GLN 3.7 0.2 - - - -
146D ASP* 1.3 100.2 + - - +
148D MET* 1.3 68.0 + - - +
294D VAL* 4.3 5.6 - - + -
295D LEU 3.4 11.0 - - - +
296D MET* 4.1 14.1 - - + -
300D ALA* 4.1 7.6 - - + -
304D LEU* 4.3 9.0 - - + -
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Residues in contact with MET 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D VAL* 4.2 3.4 - - - -
88D GLU* 3.4 41.3 - - + +
89D ALA* 4.5 0.9 - - - +
90D TYR* 3.8 29.4 - - + +
136D ALA* 3.8 37.5 - - + +
139D SER* 3.9 17.5 - - - -
140D LEU* 4.3 9.3 - - + +
145D GLN* 3.9 17.7 - - + -
147D VAL* 1.3 79.7 - - - +
149D VAL* 1.3 66.7 + - - +
294D VAL* 3.7 4.3 - - - +
295D LEU* 2.8 36.3 + - + +
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D ILE* 4.1 23.8 - - + -
75D ALA* 5.4 0.4 - - + -
76D ILE* 3.7 25.6 - - + -
86D VAL* 3.4 24.5 - - + -
88D GLU 3.2 6.3 + - - +
89D ALA* 3.3 12.5 - - + +
90D TYR* 3.0 24.7 + - - +
91D MET* 5.2 2.0 - - - -
113D LEU* 5.0 0.4 - - + -
148D MET* 1.3 79.4 - - - +
150D ALA* 1.3 66.5 + - - +
292D ALA* 3.9 24.7 - - + -
293D LEU 3.3 10.8 - - - +
294D VAL* 4.3 7.0 - - + -
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Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D TYR* 3.2 7.6 - - + +
91D MET* 4.3 3.4 - - - -
132D ALA 3.8 10.3 - - - +
133D ILE* 3.7 32.1 - - + -
136D ALA* 3.8 13.5 - - + -
148D MET 4.2 0.2 - - - -
149D VAL* 1.3 76.0 - - - +
151D GLY* 1.3 59.8 + - - +
292D ALA* 3.6 1.1 - - - -
293D LEU* 2.8 36.0 + - - +
295D LEU* 3.9 10.1 - - + +
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Residues in contact with GLY 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D TYR 3.2 6.7 + - - -
91D MET* 3.5 8.8 - - - -
92D GLY* 2.8 25.5 + - - -
129D GLY* 3.8 5.2 - - - -
132D ALA* 3.4 12.6 - - - +
133D ILE* 4.8 0.2 - - - -
150D ALA* 1.3 75.5 - - - +
152D GLY* 1.3 52.5 + - - -
291D ALA 3.2 13.2 - - - -
392D ALA* 3.8 19.3 - - - -
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Residues in contact with GLY 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D MET* 3.6 6.1 - - - +
92D GLY 3.2 8.3 - - - -
129D GLY* 4.4 0.9 - - - -
151D GLY* 1.3 74.4 - - - -
153D MET* 1.3 61.9 + - - +
290D ALA* 3.2 3.5 - - - +
291D ALA 2.9 33.2 + - - +
388D GLY 3.2 17.7 - - - -
389D MET* 3.8 10.5 - - - +
392D ALA* 3.9 3.6 - - - +
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Residues in contact with MET 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ALA* 3.7 28.0 - - + +
65D THR* 4.1 6.7 - - + -
68D GLY* 4.1 4.5 - - - -
91D MET* 4.0 17.9 - - + -
92D GLY 2.8 17.0 + - - +
93D ASN* 3.3 31.4 + - + +
103D PRO* 3.6 43.5 - - + +
104D THR* 3.8 11.0 - - - +
107D ALA* 3.9 18.8 - - + -
152D GLY* 1.3 74.6 - - - +
154D GLU* 1.3 66.7 + - - +
289D GLY 3.5 6.7 - - - +
290D ALA* 3.8 11.4 - - + -
388D GLY* 3.8 2.9 + - - -
389D MET* 4.3 2.7 - - - -
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Residues in contact with GLU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ALA* 3.9 8.1 - - - +
67D LEU* 4.2 1.7 - - - +
93D ASN* 3.1 11.4 + - - -
94D VAL* 2.9 21.8 + - - +
95D LEU* 3.0 35.2 + - + +
99D GLU* 4.7 0.3 - - - +
153D MET* 1.3 74.2 - - - +
155D SER* 1.3 64.4 + - - +
156D MET* 3.8 23.1 - - + +
159D VAL* 5.2 0.9 - - + +
288D ASP* 3.2 3.7 - - - +
289D GLY 3.0 34.0 + - - +
386D PRO* 3.8 22.7 - - + +
387D ILE* 3.6 13.2 - - + +
388D GLY* 2.8 24.9 + - - +
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Residues in contact with SER 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LEU 3.5 7.2 + - - -
64D ALA* 3.4 34.0 - - - +
67D LEU* 4.7 1.6 - - - -
99D GLU* 5.1 1.9 + - - +
154D GLU* 1.3 75.3 + - - +
156D MET* 1.3 63.7 + - - +
158D ASN* 2.9 40.9 + - - -
159D VAL* 3.4 15.0 + - - +
288D ASP* 3.4 15.7 + - - -
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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