Contacts of the strand formed by residues 241 - 256 (chain A) in PDB entry 3O7O
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 ALA 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ALA 3.6 2.7 - - - +
50A ASP* 3.5 3.3 - - - +
51A ILE* 2.8 51.3 + - + +
54A LEU* 3.8 9.3 - - + +
107A GLU* 3.3 4.3 - - - -
110A LEU* 4.0 15.5 - - + -
233A PHE* 4.0 19.7 - - + -
238A THR* 4.7 0.2 - - + -
240A SER* 1.3 75.8 - - - +
242A GLN* 1.3 60.7 + - - +
243A PHE* 4.1 8.5 - - + -
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Residues in contact with GLN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA 3.4 9.0 - - - +
50A ASP* 3.5 33.3 + - + +
106A HIS* 3.7 0.2 - - - -
107A GLU* 2.8 54.5 + - + +
110A LEU* 4.2 1.1 - - - +
241A ALA* 1.3 71.2 - - - +
243A PHE* 1.3 60.9 + - - +
266A BR 3.8 3.2 - - - +
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Residues in contact with PHE 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PHE* 3.6 28.5 - + - -
48A ASP* 3.6 1.9 - - - +
49A ALA* 2.8 48.6 + - + +
67A PRO* 4.1 0.7 - - + -
104A ILE* 5.9 0.2 - - + -
105A HIS* 3.3 20.9 - - - +
106A HIS* 3.7 13.9 - - + +
110A LEU* 3.6 17.5 - - + -
112A LEU* 3.6 14.8 - - + -
231A THR* 3.7 22.7 - - - -
233A PHE* 3.5 47.1 - + - -
241A ALA* 4.1 6.3 - - + -
242A GLN* 1.3 74.5 - - - +
244A GLY* 1.3 68.1 + - - +
245A TRP* 4.5 1.3 - + - -
266A BR 4.4 3.8 - - - -
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Residues in contact with GLY 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PHE* 3.1 16.8 - - - -
48A ASP* 4.1 0.7 - - - -
104A ILE* 3.8 2.9 - - - +
105A HIS* 3.0 48.6 + - - +
243A PHE* 1.3 84.5 - - - +
245A TRP* 1.3 66.7 + - - +
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Residues in contact with TRP 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A MET* 4.0 11.2 - - + -
45A ILE* 3.8 31.2 - - + -
46A THR* 3.3 14.8 - - - -
47A PHE* 2.9 61.8 + + + +
48A ASP* 5.1 0.2 - - - +
67A PRO* 3.6 29.0 + - - +
68A GLU* 4.0 5.8 - - - -
103A ASP 3.3 12.8 - - - +
104A ILE* 3.8 15.3 - - + -
105A HIS* 3.7 5.8 + - - -
231A THR* 3.0 41.5 + - + +
243A PHE* 4.5 2.9 - + - -
244A GLY* 1.3 78.2 - - - +
246A LYS* 1.3 62.0 + - - +
247A PHE* 3.3 42.0 - + + -
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LYS* 3.9 29.9 - - + +
45A ILE 3.4 5.6 - - - -
46A THR* 3.8 16.6 - - + -
102A PHE* 3.3 4.7 - - - -
103A ASP* 3.0 52.1 + - + +
105A HIS* 6.1 1.6 - - + +
245A TRP* 1.3 76.1 - - - +
247A PHE* 1.3 67.5 + - - +
248A GLU* 3.4 25.9 + - + +
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Residues in contact with PHE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 3.3 6.7 - - + -
44A LYS* 3.4 5.4 - - - +
45A ILE* 2.8 41.7 + - + -
69A PHE* 3.4 27.6 - + + -
100A VAL* 4.0 15.9 - - + -
101A SER 3.3 5.4 - - - +
102A PHE* 3.5 24.0 - - + -
104A ILE* 4.2 7.6 - - + -
114A PHE* 3.3 38.6 - + - -
229A ILE* 3.9 10.8 - - + -
230A GLY* 4.4 5.6 - - - -
245A TRP* 3.3 56.3 - + - -
246A LYS* 1.3 73.5 - - - +
248A GLU* 1.3 61.9 + - - +
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Residues in contact with GLU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 3.7 10.1 - - - -
43A GLU* 4.6 7.2 - - - +
44A LYS* 3.6 29.3 - - + +
100A VAL* 3.6 4.0 - - - +
101A SER* 2.8 38.3 + - - +
246A LYS* 3.4 29.6 + - + -
247A PHE* 1.3 78.3 - - - +
249A ASN* 1.4 77.2 + - - +
250A PHE 3.3 3.2 + - - -
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Residues in contact with ASN 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 4.0 4.4 - - - +
16A ASN* 4.7 4.0 - - - -
43A GLU 4.6 2.6 + - - -
99A GLU* 3.6 18.7 - - - +
100A VAL* 3.8 4.9 + - - -
101A SER* 2.9 28.0 + - - +
194A ARG* 3.5 33.3 + - - +
248A GLU* 1.4 81.5 - - - +
250A PHE* 1.3 61.5 + - - +
251A SER* 3.8 0.9 + - - -
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Residues in contact with PHE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 3.4 43.3 - + + -
16A ASN* 3.0 25.2 + - - +
18A ILE* 4.0 23.5 - - + +
20A LEU* 3.7 32.1 - - + -
69A PHE* 3.8 17.3 - + - -
71A TYR* 5.1 4.0 - - + -
98A VAL* 4.3 3.6 - - + -
99A GLU 3.3 16.4 - - - -
100A VAL* 4.2 10.8 - - + -
227A TRP* 6.0 0.7 - + - -
229A ILE* 3.5 25.6 - - + -
248A GLU 3.3 1.5 - - - -
249A ASN* 1.3 75.2 - - - +
251A SER* 1.3 63.1 + - - +
252A ILE* 3.4 29.8 - - + -
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Residues in contact with SER 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASN* 6.2 0.4 - - - -
18A ILE* 3.8 10.8 - - - -
97A SER 4.0 0.6 - - - +
98A VAL* 3.6 0.3 - - - -
99A GLU* 2.8 58.5 + - - +
196A LYS* 6.0 0.3 - - - -
249A ASN 3.8 0.8 + - - -
250A PHE* 1.3 76.6 - - - +
252A ILE* 1.3 68.7 + - - +
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Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 3.9 30.0 - - + +
71A TYR* 3.9 41.5 - - + +
85A LYS* 6.0 3.8 - - - -
96A PHE* 4.5 16.6 - - + -
97A SER 3.2 6.1 - - - +
98A VAL* 4.0 19.7 - - + -
227A TRP* 5.7 1.8 - - + -
250A PHE* 3.4 28.7 - - + -
251A SER* 1.3 78.6 - - - +
253A ASP* 1.3 64.4 + - - +
254A LEU* 4.9 4.9 - - + +
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Residues in contact with ASP 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER* 3.8 3.5 + - - +
96A PHE* 3.4 5.5 - - - -
97A SER* 2.9 48.6 + - - +
252A ILE* 1.3 75.5 - - - +
254A LEU* 1.3 69.3 + - - +
255A GLU* 3.9 10.8 + - - +
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TYR* 5.6 1.3 - - + -
85A LYS* 4.0 47.5 + - + +
86A LEU* 4.1 19.1 - - + -
88A VAL* 4.4 9.0 - - + -
93A MET* 4.2 22.2 - - + -
95A SER 3.7 10.8 - - - +
96A PHE* 3.7 25.7 - - + -
252A ILE* 4.9 6.4 - - + +
253A ASP* 1.3 80.3 + - - +
255A GLU* 1.3 69.3 + - - +
256A VAL* 3.8 24.7 + - + +
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Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A MET* 3.8 2.6 - - - -
94A LYS* 2.8 67.7 + - + +
95A SER* 2.9 32.5 + - - +
253A ASP* 3.9 11.1 + - - +
254A LEU* 1.3 72.4 - - - +
256A VAL* 1.3 65.0 + - - +
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LYS* 6.2 2.0 - - + -
88A VAL* 4.9 9.9 - - + -
92A SER* 3.3 29.4 - - - +
94A LYS* 4.7 3.3 - - - +
254A LEU* 3.8 30.7 + - + +
255A GLU* 1.3 83.8 - - - +
257A ARG* 1.3 75.0 + - - +
258A GLU* 3.8 5.5 + - - +
259A HIS* 5.9 2.0 - - + -
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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