Contacts of the strand formed by residues 95 - 105 (chain A) in PDB entry 3NNJ
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 LEU 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LEU* 4.1 18.7 - - + +
87A LEU* 3.6 38.8 - - + +
88A ASN* 2.7 23.2 + - - +
91A THR* 4.2 3.1 - - - +
93A LYS* 4.1 11.9 - - + -
94A ASN* 1.3 76.3 + - - +
96A MSE 1.3 58.6 + - - +
97A ILE 4.3 0.2 - - - -
129A PHE* 3.4 35.9 - - + -
131A ALA* 5.2 0.2 - - + -
221A PHE* 4.3 13.5 - - + -
248A LEU* 4.4 21.1 - - + -
249A VAL 3.6 11.0 - - - +
315A ARG 4.0 0.8 - - - +
316A MSE 3.8 22.9 - - - +
317A ALA 4.4 1.9 + - - -
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Residues in contact with MSE 96 (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 LEU* 1.3 76.0 - - - +
97A ILE* 1.3 68.6 + - - +
98A MSE 3.4 26.3 + - + +
248A LEU* 3.2 4.0 - - - -
249A VAL* 2.8 49.1 + - + +
250A ASP 4.1 1.3 - - - +
251A TYR* 2.9 64.4 - - + +
302A LEU* 5.3 0.7 - - - -
303A ARG* 4.0 14.4 - - + -
308A VAL* 4.2 2.9 - - - -
312A LEU* 3.9 17.5 - - + -
315A ARG* 3.5 11.0 - - + -
316A MSE 3.7 19.7 - - + -
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Residues in contact with ILE 97 (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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77A SER* 4.0 30.3 - - - +
80A ILE* 3.5 31.2 - - + -
81A GLN 4.4 1.1 - - - +
84A LEU* 4.1 10.5 - - + -
96A MSE 1.3 70.5 - - - +
98A MSE 1.3 67.4 + - - +
99A HIS* 4.0 4.7 - - - +
100A ASN* 3.6 24.5 - - - +
246A ILE* 4.0 5.2 - - + -
248A LEU* 3.4 22.7 - - + -
314A ALA 4.6 5.6 - - - +
315A ARG* 2.9 53.4 + - + +
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Residues in contact with MSE 98 (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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70A LEU* 4.9 6.1 - - - +
96A MSE 3.6 31.9 - - + +
97A ILE* 1.3 93.9 - - - +
99A HIS* 1.3 67.8 + - + +
123A PHE* 5.0 8.5 - - + -
247A ARG* 2.8 21.9 + - + +
249A VAL* 3.5 37.7 - - + -
285A VAL* 4.1 19.0 - - + +
288A MSE 5.5 4.8 - - - +
302A LEU* 4.3 17.5 - - + -
308A VAL* 3.6 34.1 - - + -
315A ARG* 3.0 23.7 + - - +
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Residues in contact with HIS 99 (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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69A ASP* 3.5 23.6 + - - -
70A LEU* 3.8 20.4 - - - -
74A ASP* 6.1 0.7 - - - -
97A ILE* 3.8 2.6 - - - +
98A MSE 1.3 84.8 - - + +
100A ASN* 1.3 93.0 + - - +
101A ALA* 3.4 20.2 - - + +
245A VAL 3.9 0.7 - - - +
246A ILE* 3.4 1.4 - - - +
247A ARG* 3.0 55.9 + - - +
283A ASP* 5.3 0.7 - - - -
284A SER* 3.5 25.5 + - - -
285A VAL* 3.4 20.9 - - + -
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Residues in contact with ASN 100 (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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69A ASP* 4.5 3.3 - - - +
70A LEU 5.4 0.8 + - - -
73A TYR* 3.5 46.1 + - + +
74A ASP* 4.0 11.7 + - - +
76A VAL* 4.4 5.6 - - + +
77A SER* 3.0 32.3 + - - +
80A ILE* 5.1 0.7 - - - +
97A ILE* 3.6 8.2 - - - +
99A HIS* 1.3 98.4 + - - +
101A ALA* 1.3 62.4 + - - +
244A PHE* 5.1 1.8 - - + -
245A VAL 3.9 3.6 - - - -
246A ILE* 3.2 33.7 - - + +
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Residues in contact with ALA 101 (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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69A ASP* 5.5 2.0 - - - +
73A TYR* 4.3 3.8 - - - -
99A HIS* 3.4 22.0 - - + +
100A ASN* 1.3 75.6 - - - +
102A LEU* 1.3 62.3 + - - +
103A PHE* 3.8 22.4 - - + -
244A PHE* 3.2 13.2 - - - -
245A VAL* 3.0 33.1 + - + +
247A ARG* 5.6 2.5 - - - +
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Residues in contact with LEU 102 (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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37A LEU* 4.0 24.9 - - + -
73A TYR* 3.6 36.0 - - + +
101A ALA* 1.3 75.3 - - - +
103A PHE* 1.3 73.5 + - - +
104A SER* 4.3 9.4 + - - +
137A LEU* 3.9 25.4 - - + -
242A ARG* 5.0 5.2 - - + -
243A ALA 3.4 20.0 - - - +
244A PHE* 4.0 13.7 - - + -
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Residues in contact with PHE 103 (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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101A ALA* 3.8 22.2 - - + -
102A LEU* 1.3 80.4 - - - +
104A SER* 1.3 61.2 + - - +
105A VAL* 5.8 1.3 - - + -
241A ARG 3.0 3.6 - - - +
242A ARG* 3.3 1.2 - - - -
243A ALA* 2.8 46.9 + - + +
245A VAL* 3.3 42.6 - - + -
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Residues in contact with SER 104 (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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102A LEU* 4.2 11.7 + - - +
103A PHE* 1.3 71.3 - - - +
105A VAL* 1.3 72.2 + - - +
240A LEU* 4.3 16.7 - - - +
241A ARG 2.6 13.2 - - - -
242A ARG* 4.0 20.6 - - - -
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Residues in contact with VAL 105 (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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103A PHE* 5.8 2.0 - - + -
104A SER* 1.3 84.1 - - - +
106A GLU* 1.3 68.6 + - - +
109A HIS* 3.7 30.7 - - + +
240A LEU* 3.3 11.0 - - - -
241A ARG* 2.7 83.9 + - + +
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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