Contacts of the strand formed by residues 46 - 54 (chain A) in PDB entry 4I6N
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 ILE 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ILE* 3.6 32.3 - - + -
43A LEU* 3.9 31.4 - - + +
44A LYS* 3.6 13.5 - - + +
45A PRO* 1.3 75.6 - - - +
47A HIS* 1.3 63.7 + - - +
48A GLY 3.5 22.9 - - - +
49A PHE* 4.2 11.9 - - + -
167A PRO* 5.1 1.2 - - - +
194A TRP* 3.2 34.1 + - + +
195A THR* 4.1 12.8 - - + -
220A ALA* 4.0 12.3 - - + -
221A VAL 3.8 6.5 - - - +
222A ILE* 4.2 2.9 - - + -
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Residues in contact with HIS 47 (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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28A LEU* 3.4 27.2 - - + +
45A PRO* 3.7 12.4 + - + +
46A ILE* 1.3 74.4 + - - +
48A GLY* 1.3 57.4 + - - +
93A LEU* 4.3 4.1 - - + +
97A CYS* 4.5 15.9 - - - -
99A HIS* 3.5 51.1 - + + +
102A VAL* 4.4 6.3 - - + +
166A VAL* 3.5 21.3 - - - +
167A PRO* 3.7 8.4 - - - +
194A TRP* 4.1 2.5 - - - -
221A VAL* 2.8 19.2 + - + +
222A ILE* 3.6 16.8 - - - -
223A SER* 2.9 22.6 + - - -
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Residues in contact with GLY 48 (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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46A ILE* 3.5 9.6 - - - +
47A HIS* 1.3 80.3 - - - +
49A PHE* 1.3 64.4 + - - -
93A LEU* 3.9 15.7 - - - -
165A TYR 3.1 14.6 - - - -
194A TRP* 3.7 8.7 - - - -
220A ALA* 3.6 0.5 - - - -
221A VAL* 2.9 25.5 + - - +
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Residues in contact with PHE 49 (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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33A LEU* 4.1 18.2 - - + -
40A ILE* 4.3 6.3 - - + -
46A ILE* 4.2 12.1 - - + -
48A GLY* 1.3 73.9 - - - -
50A ILE* 1.3 65.2 + - - +
51A PHE 4.2 0.2 - - - -
93A LEU* 3.9 2.3 - - - +
164A THR* 3.3 4.9 - - - -
165A TYR* 2.8 43.4 + - + +
194A TRP* 3.5 25.1 - + - -
195A THR* 3.8 32.1 - - + -
198A ALA* 3.9 20.4 - - + -
199A ILE* 4.4 9.9 - - + -
202A ILE* 4.9 2.9 - - + -
218A LEU* 3.9 23.3 - - + -
219A MSE 3.2 16.6 - - - +
220A ALA* 4.0 20.9 - - + -
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Residues in contact with ILE 50 (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 PHE* 4.0 28.5 - - + -
30A VAL* 4.7 7.0 - - + -
49A PHE* 1.3 76.8 - - - +
51A PHE* 1.3 61.6 + - - +
89A ALA* 4.9 3.6 - - + -
90A LEU* 4.1 13.7 - - + -
93A LEU* 4.0 10.3 - - + -
162A PHE* 3.8 23.8 - - + -
163A VAL 3.3 9.4 - - - +
164A THR* 4.1 6.7 - - - +
217A ASN 3.9 0.7 - - - +
218A LEU* 3.6 3.7 - - - +
219A MSE 2.9 60.3 + - + +
221A VAL* 3.6 26.9 - - + -
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Residues in contact with PHE 51 (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 PHE 4.2 0.2 - - - -
50A ILE* 1.3 75.3 - - - +
52A LEU* 1.3 67.7 + - - +
53A PHE* 3.7 29.6 - + + -
161A HIS 3.5 1.2 - - - +
162A PHE* 3.4 4.1 - - - -
163A VAL* 2.8 34.2 + - + +
165A TYR* 3.8 28.3 - + + -
202A ILE* 3.7 38.4 - - + -
205A LYS* 3.8 19.3 - - + -
206A ILE* 4.1 6.3 - - + -
216A PHE* 3.5 36.1 - + + -
217A ASN 3.2 17.5 - - - -
218A LEU* 4.2 13.2 - - + -
8B LEU* 4.7 6.3 - - + -
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Residues in contact with LEU 52 (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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11A SER* 4.1 1.8 - - - -
51A PHE* 1.3 80.4 - - - +
53A PHE* 1.3 68.4 + - - +
160A PHE* 3.9 26.7 - - + -
161A HIS 3.1 10.5 - - - +
162A PHE* 3.5 44.2 - - + -
215A ARG 4.5 0.9 - - - +
216A PHE* 3.3 7.1 - - - -
217A ASN* 2.9 46.8 + - + +
219A MSE 6.3 0.2 - - + -
73B LEU* 3.6 44.2 - - + +
75B GLY* 4.0 6.7 - - - -
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Residues in contact with PHE 53 (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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51A PHE* 3.7 18.8 - + + -
52A LEU* 1.3 80.0 - - - +
54A ARG* 1.3 65.1 + - - +
55A TRP* 3.4 22.6 + + - -
59A GLU* 3.5 19.5 - - - -
160A PHE* 3.4 5.8 - - - -
161A HIS* 2.9 51.8 + + + -
163A VAL* 3.5 32.8 - - + -
176A ASP* 4.6 1.6 - - - -
205A LYS* 3.8 24.5 - - + -
209A TYR* 3.3 23.8 - - - +
215A ARG 4.1 8.5 - - - -
216A PHE* 3.8 16.8 - - + -
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Residues in contact with ARG 54 (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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53A PHE* 1.3 71.2 - - - +
55A TRP* 1.3 67.9 + - - +
56A LEU* 3.4 19.6 + - - +
157A GLU* 2.9 39.9 + - - +
158A ASP* 4.4 7.6 - - - +
159A VAL 3.6 10.3 - - - +
160A PHE* 3.8 22.6 - - + -
209A TYR* 2.4 54.3 + - + -
213A GLU* 3.1 19.7 + - + +
215A ARG* 3.1 38.7 + - - +
216A PHE* 5.1 0.6 - - - -
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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