Contacts of the strand formed by residues 47 - 59 (chain A) in PDB entry 5ANC
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 MET 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLN* 3.7 19.1 - - + -
46A PHE* 1.3 90.4 - - - +
48A GLY* 1.3 70.4 + - - +
49A TYR* 4.1 1.6 - - + -
82A PRO* 4.3 1.9 - - - +
84A MET* 3.1 9.2 - - + +
167A THR* 3.1 39.0 - - + +
180A HIS* 4.2 23.1 - - + +
181A VAL 4.2 4.7 - - - +
182A LEU* 3.5 30.3 - - + -
343A ALA* 3.9 9.6 - - + -
344A LEU 3.7 12.6 - - - +
345A THR* 3.0 27.4 - - - +
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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 PHE* 4.0 3.0 - - - -
47A MET* 1.3 76.5 - - - +
49A TYR* 1.3 76.5 + - - -
79A ILE* 4.3 5.8 - - - -
80A GLU 3.3 11.9 - - - -
81A CYS* 3.8 17.7 - - - -
343A ALA* 4.1 0.2 - - - -
344A LEU* 3.3 27.6 + - - -
346A LEU* 4.3 4.2 - - - +
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Residues in contact with TYR 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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47A MET* 4.7 2.1 - - + +
48A GLY* 1.3 94.9 - - - -
50A LYS* 1.3 64.9 + - - +
51A ALA* 6.3 0.2 - - + -
79A ILE* 3.0 9.5 - - - +
80A GLU* 2.8 51.4 + - + +
82A PRO* 4.1 10.3 - - + -
167A THR* 2.6 43.2 + - + +
169A VAL* 3.3 21.0 - - + +
172A LEU* 4.6 7.0 - - + -
174A LEU* 4.9 9.6 - - + -
176A GLN* 3.6 27.6 - - - -
180A HIS* 3.2 30.9 - + - -
342A ARG 3.9 15.7 - - - +
343A ALA* 4.3 7.9 - - + -
344A LEU 4.8 0.7 - - - +
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Residues in contact with LYS 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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49A TYR* 1.3 74.8 - - - +
51A ALA* 1.3 62.6 + - - +
52A GLY* 3.9 15.0 - - - +
53A MET* 4.2 20.4 - - - -
77A THR* 4.5 1.1 - - + -
78A ILE 4.4 2.5 - - - +
79A ILE* 3.5 13.3 - - + +
174A LEU* 6.0 1.0 - - - +
336A VAL* 3.8 26.3 + - + -
338A GLY 2.7 26.2 + - - +
339A PRO* 3.2 27.3 - - - +
340A ARG* 3.1 29.9 - - + +
341A LYS* 4.9 0.2 - - - -
342A ARG 3.4 12.9 + - - +
344A LEU* 4.3 10.1 - - + +
3383N U 3.2 8.7 + - - -
3384N C 2.7 26.1 + - - -
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 3.5 2.8 + - + -
50A LYS* 1.3 74.9 - - - +
52A GLY* 1.3 60.8 + - - +
78A ILE* 3.6 14.9 + - - +
80A GLU* 3.4 33.2 - - + +
315A PRO* 4.2 14.6 - - - +
323A GLY* 4.2 17.8 - - - +
325A VAL* 4.5 10.0 - - + +
340A ARG* 3.9 19.6 + - - +
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Residues in contact with GLY 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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50A LYS* 3.8 13.1 - - - +
51A ALA* 1.3 75.5 - - - +
53A MET* 1.3 64.0 + - - +
78A ILE* 3.2 30.6 + - - +
315A PRO* 5.5 3.4 - - - -
340A ARG* 3.6 29.8 - - - +
3385N A 5.5 2.7 - - - -
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Residues in contact with MET 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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50A LYS* 4.2 13.7 - - - -
52A GLY* 1.3 73.2 - - - +
54A THR* 1.3 69.7 + - - +
75A ALA* 5.2 5.2 - - + -
76A VAL 3.4 11.9 - - - +
77A THR* 3.3 33.9 - - + +
78A ILE* 4.3 2.5 - - - -
315A PRO* 5.6 3.5 - - - +
334A GLY* 5.4 0.2 - - - -
335A CYS* 4.0 17.7 - - - +
370A SER* 4.2 5.2 + - - -
3383N U 3.4 26.0 - - - +
3384N C 3.7 17.0 - - - +
3385N A 3.2 58.7 + - + +
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Residues in contact with THR 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 MET* 1.3 77.8 - - - +
55A HIS* 1.3 65.7 + - - +
76A VAL* 2.8 42.3 + - - +
78A ILE* 3.9 25.8 - - + +
313A ILE* 4.5 13.7 - - + +
315A PRO* 4.8 11.4 - - + -
331A MET* 5.0 1.2 - - - -
367A ILE* 4.1 9.4 - - - +
368A ASP* 4.5 17.7 - - - +
369A THR* 5.7 1.3 - - - -
370A SER* 5.0 6.1 - - - +
3385N A 3.2 18.7 - - - +
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Residues in contact with HIS 55 (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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54A THR* 1.3 78.4 - - - +
56A VAL* 1.3 66.4 + - - +
57A VAL* 5.5 2.0 - - + -
73A VAL* 3.3 21.6 - - + +
74A GLU 3.7 11.2 - - - +
75A ALA* 4.1 0.4 - - - -
76A VAL* 4.1 1.1 - - - -
366A PHE* 5.9 1.3 - - + -
367A ILE* 3.5 5.5 - - - +
368A ASP* 2.8 62.0 + - + +
16G ALA* 3.3 39.4 + - + +
17G ARG* 4.5 1.0 - - - +
3385N A 2.9 46.5 + - + +
3386N C 4.1 16.3 - - - -
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Residues in contact with VAL 56 (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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55A HIS* 1.3 81.7 + - - +
57A VAL* 1.3 78.6 + - - +
58A ARG* 3.4 39.0 + - - +
73A VAL* 3.3 4.0 - - - -
74A GLU* 2.8 43.3 + - + +
76A VAL* 3.7 24.0 - - + -
286A TYR* 5.1 0.4 - - + -
331A MET* 4.4 1.8 - - + -
364A LEU* 4.0 5.4 - - + -
366A PHE 3.5 11.7 - - - +
367A ILE* 3.8 17.7 - - + -
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Residues in contact with VAL 57 (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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55A HIS* 5.5 4.0 - - + +
56A VAL* 1.3 79.4 - - - +
58A ARG* 1.3 64.5 + - - +
71A GLU* 3.4 29.6 - - + +
72A ILE 3.3 10.5 - - - +
73A VAL* 3.8 21.8 - - + -
365A LYS* 2.8 51.2 + - + -
366A PHE* 3.0 36.3 + - + +
1G MET* 4.5 8.1 - - + +
15G PRO 4.7 2.9 - - - +
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Residues in contact with ARG 58 (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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56A VAL* 3.4 24.4 - - - +
57A VAL* 1.3 74.5 - - - +
59A ASP* 1.3 66.2 - - - +
60A LEU* 3.5 1.7 + - + -
72A ILE* 3.1 27.0 + - - +
74A GLU* 3.3 35.4 - - + +
286A TYR* 3.1 40.7 - - - +
331A MET* 3.2 32.5 - - - +
362A ILE* 3.6 21.1 - - + +
363A THR 3.0 28.5 + - - +
364A LEU* 3.5 30.8 - - - +
365A LYS* 4.6 1.3 - - - +
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Residues in contact with ASP 59 (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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58A ARG* 1.3 73.8 - - - +
60A LEU* 1.3 62.4 + - - +
61A GLU* 4.2 5.2 + - - -
69A LYS* 5.1 13.9 - - + -
70A LYS* 3.5 13.9 - - - +
71A GLU* 3.2 25.2 + - - -
306A PHE* 4.6 11.3 - - - -
362A ILE* 4.5 6.8 - - - +
363A THR* 3.8 18.8 + - - +
365A LYS* 3.4 34.1 + - - +
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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