Contacts of the strand formed by residues 42 - 50 (chain B) in PDB entry 3N2N
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 GLY 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B TYR* 3.4 11.4 - - - +
41B GLY* 1.3 81.5 - - - +
43B PHE* 1.3 60.3 + - - -
44B ASP* 5.1 2.0 - - - -
77B GLN 5.1 2.0 - - - -
79B ARG* 6.3 0.7 - - - -
139B TYR* 5.5 1.1 - - - -
140B ARG 3.0 6.1 + - - -
141B THR* 3.2 18.6 + - - -
142B ALA 2.9 21.3 + - - -
219B SER* 5.7 0.4 - - - -
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Residues in contact with PHE 43 (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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40B TYR* 5.6 0.2 - - + -
42B GLY* 1.3 74.1 - - - +
44B ASP* 1.3 68.4 + - - +
45B LEU* 4.7 4.5 - - + -
77B GLN 3.7 17.3 + - - +
78B LEU* 3.6 25.4 - - + -
79B ARG* 2.9 28.6 + - - +
141B THR* 3.9 0.2 - - - +
142B ALA 3.4 10.8 - - - -
144B VAL* 3.9 26.0 - - + -
212B ILE* 3.7 39.7 - - + -
215B ILE* 3.6 44.0 - - + -
216B LEU* 4.0 18.4 - - + -
219B SER* 4.8 8.1 - - - +
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Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLY* 5.1 1.0 - - - -
43B PHE* 1.3 80.8 + - - +
45B LEU* 1.3 61.1 + - - +
46B TYR* 3.7 21.5 + - + +
79B ARG* 3.0 40.3 + - - +
95B LEU* 3.4 18.7 - - + +
134B GLU* 3.9 12.0 - - - +
141B THR* 3.3 24.0 + - + +
142B ALA 2.8 10.0 + - - +
143B SER* 3.5 4.0 + - - +
144B VAL* 2.8 28.2 + - - +
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Residues in contact with LEU 45 (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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43B PHE* 4.7 5.4 - - + -
44B ASP* 1.3 71.4 - - - +
46B TYR* 1.3 61.5 + - - +
47B PHE* 3.6 33.4 + - + -
69B LEU* 5.7 1.1 - - + -
78B LEU* 3.8 26.0 - - + -
79B ARG 2.8 17.0 + - - +
80B MET* 3.0 8.8 - - + +
81B SER 2.9 25.3 + - - +
95B LEU* 4.2 0.8 - - - +
144B VAL* 3.4 30.1 - - + +
146B ILE* 3.7 24.2 - - + +
212B ILE* 4.0 25.4 - - + -
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Residues in contact with TYR 46 (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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44B ASP* 3.7 24.4 + - + +
45B LEU* 1.3 72.3 - - - +
47B PHE* 1.3 62.5 + - - +
48B ILE* 3.7 1.6 + - + -
81B SER* 3.8 19.1 - - - -
83B ILE* 4.5 5.6 - - + -
95B LEU* 3.4 29.8 - - + +
127B ALA* 4.2 19.7 - - + -
130B GLN* 3.7 31.8 - - + -
131B ILE* 3.5 42.2 + - + +
134B GLU* 3.8 6.6 - - - +
143B SER* 4.4 6.6 + - - -
144B VAL 2.7 22.0 + - - +
145B ILE* 3.4 13.5 - - + +
146B ILE 2.9 26.9 + - - +
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Residues in contact with PHE 47 (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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45B LEU* 3.6 33.2 - - + -
46B TYR* 1.3 73.1 - - - +
48B ILE* 1.3 60.5 + - - +
49B LEU* 3.9 17.9 - - + -
65B PHE* 4.3 3.6 - + - -
66B VAL* 3.8 30.1 - - + -
69B LEU* 3.9 26.5 - - + -
70B ALA 5.5 0.4 - - - -
80B MET* 4.1 14.1 - - + -
81B SER 2.9 13.4 + - - +
82B PHE* 3.7 33.9 - + + -
83B ILE* 2.8 34.4 + - - +
146B ILE* 3.5 32.3 - - + -
148B LEU* 4.8 0.7 - - + -
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Residues in contact with ILE 48 (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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46B TYR 4.4 2.7 - - - +
47B PHE* 1.3 75.4 - - - +
49B LEU* 1.3 60.1 + - - +
83B ILE* 3.5 13.2 - - + -
85B PHE* 3.7 27.0 - - + -
120B MET* 4.8 0.2 - - + -
123B GLY* 3.6 37.2 - - - +
124B PHE* 3.8 27.6 - - + +
127B ALA* 3.9 11.7 - - + -
145B ILE* 3.7 26.9 - - + -
146B ILE 2.8 11.3 + - - +
147B ALA* 3.3 9.7 - - + +
148B LEU 2.9 28.9 + - - +
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Residues in contact with LEU 49 (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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47B PHE* 4.0 18.4 - - + -
48B ILE* 1.3 82.1 - - - +
50B ASP* 1.3 63.4 + - - +
51B LYS* 3.3 1.2 + - - +
59B TRP* 4.0 21.1 - - + -
62B ILE* 4.0 4.9 - - + -
63B TYR* 6.2 0.7 - - - -
66B VAL* 3.6 29.4 - - + -
82B PHE* 5.1 2.9 - - + -
83B ILE 2.7 18.9 + - - +
84B VAL* 3.4 4.7 - - + +
85B PHE* 2.9 29.3 + - - -
109B LEU* 3.8 38.6 - - + -
148B LEU* 3.9 24.5 - - + -
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Residues in contact with ASP 50 (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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49B LEU* 1.3 68.7 - - - +
51B LYS* 1.3 56.6 + - - +
52B SER* 2.5 39.8 + - - -
55B VAL* 3.2 22.5 - - + +
59B TRP* 3.3 15.2 - - - -
62B ILE* 3.8 5.4 - - + +
85B PHE* 3.4 21.6 - - + -
118B THR* 3.6 11.8 - - - +
148B LEU* 3.0 24.6 + - - +
149B THR* 2.6 28.9 + - - -
150B ASP* 3.8 7.3 - - - +
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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