Contacts of the strand formed by residues 57 - 69 (chain A) in PDB entry 5IXM
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A TYR* 4.1 1.9 - - - -
53A LEU* 4.0 1.7 - - - -
54A LEU* 2.9 35.7 + - - +
55A ALA 3.0 2.3 - - - -
56A PRO* 1.3 78.8 - - - +
58A SER* 1.3 60.7 + - - -
91A HIS* 3.4 13.2 - - - -
92A SER 3.3 11.7 - - - -
93A GLY* 3.6 7.0 - - - -
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Residues in contact with SER 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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52A TYR 3.5 10.5 - - - -
53A LEU* 3.8 20.1 - - - +
57A GLY* 1.3 73.7 - - - -
59A GLY* 1.3 57.9 + - - +
91A HIS* 3.5 3.9 + - - -
92A SER* 2.9 39.8 + - - -
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Residues in contact with GLY 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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51A ARG* 3.5 2.4 - - - +
52A TYR* 2.9 53.1 + - - +
58A SER* 1.3 75.9 - - - +
60A THR* 1.3 66.8 + - - -
90A GLY 3.1 13.2 - - - -
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Residues in contact with THR 60 (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 GLU* 3.9 16.4 - - + +
50A PHE 3.5 4.3 - - - -
51A ARG* 3.5 20.6 - - + +
52A TYR* 3.9 1.0 - - - -
59A GLY* 1.3 77.9 + - - -
61A MET* 1.3 73.5 + - - +
88A TYR* 3.4 14.8 - - + -
89A TRP* 3.5 0.5 - - - -
90A GLY 2.9 33.7 + - - -
121A TYR* 3.7 24.5 - - + +
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Residues in contact with MET 61 (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 GLU* 3.5 1.7 - - - -
50A PHE* 2.9 61.3 + - + +
52A TYR* 4.2 9.2 - - + -
60A THR* 1.3 77.4 - - - +
62A ALA* 1.3 65.8 + - - +
87A TYR* 3.2 31.9 - - + +
88A TYR 3.2 6.3 - - - +
89A TRP* 3.5 38.6 - - + +
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Residues in contact with ALA 62 (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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48A ASN 3.2 11.9 - - - +
49A GLU* 4.7 2.0 - - + -
61A MET* 1.3 78.1 - - - +
63A LEU* 1.3 61.3 + - - +
64A ASP* 4.3 3.4 - - - +
86A LEU* 4.3 3.6 - - + -
87A TYR* 3.3 11.0 - - - -
88A TYR* 2.9 39.0 + - + -
121A TYR* 3.6 37.5 - - + +
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Residues in contact with LEU 63 (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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48A ASN* 2.9 61.3 + - + +
62A ALA* 1.3 73.8 - - - +
64A ASP* 1.3 71.5 + - - +
65A TRP* 5.1 7.2 - - + -
85A TRP* 5.0 8.3 - - + -
86A LEU 3.3 19.3 - - - +
87A TYR* 4.6 17.5 - - + -
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Residues in contact with ASP 64 (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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45A GLN* 4.0 7.0 + - - +
46A TRP 3.3 3.8 - - - +
47A GLN* 3.6 37.7 + - - +
48A ASN 4.0 2.4 + - - +
62A ALA* 5.0 2.9 - - - +
63A LEU* 1.3 82.6 + - - +
65A TRP* 1.3 61.6 + - - +
66A LEU 4.3 0.2 - - - -
85A TRP* 3.1 9.0 - - - +
86A LEU* 2.9 41.1 + - + +
113A TYR* 3.1 26.8 + - - +
118A THR 4.6 0.7 - - - +
119A SER* 4.5 15.1 - - - -
121A TYR* 5.8 2.8 - - - -
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Residues in contact with TRP 65 (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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45A GLN* 3.6 3.3 - - - +
46A TRP* 2.9 62.3 + + + +
48A ASN* 5.3 2.9 - - - +
63A LEU* 5.1 10.8 - - + -
64A ASP* 1.3 75.4 - - - +
66A LEU* 1.3 59.4 + - - +
67A PRO* 3.5 34.4 - - + +
83A THR* 3.5 27.1 - - + +
84A ARG 3.7 2.7 - - - -
85A TRP* 4.7 8.1 - + + -
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Residues in contact with LEU 66 (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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39A MET* 4.0 3.4 - - + -
42A ARG* 3.7 35.4 - - + +
43A GLY* 3.7 10.3 - - - -
44A LEU 3.3 39.7 - - - +
45A GLN* 3.7 14.8 - - + +
64A ASP 4.3 0.2 - - - -
65A TRP* 1.3 73.1 - - - +
67A PRO* 1.3 66.1 - - + +
68A ASN 4.9 3.8 - - - +
69A ASP* 4.0 14.1 - - + +
82A ALA 4.0 1.0 - - - +
83A THR* 3.4 2.9 - - - -
84A ARG* 2.8 51.4 + - + +
117A LEU* 4.0 16.2 - - + -
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Residues in contact with PRO 67 (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 LEU* 3.2 20.4 - - + +
46A TRP* 5.2 1.8 - - + +
65A TRP* 3.5 42.1 - - + +
66A LEU* 1.3 85.9 - - + +
68A ASN* 1.3 78.0 + - - +
81A ASN 4.3 1.2 - - - +
82A ALA 3.1 16.5 - - - +
83A THR* 3.1 24.5 + - + +
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Residues in contact with ASN 68 (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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42A ARG 3.3 11.8 - - - +
43A GLY* 4.5 4.3 - - - -
66A LEU* 3.7 4.9 - - - +
67A PRO* 1.3 95.2 - - - +
69A ASP* 1.3 63.8 + - - +
70A ARG* 3.4 11.5 + - + +
81A ASN* 4.4 23.8 - - + +
82A ALA 4.1 0.7 - - - -
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Residues in contact with ASP 69 (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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42A ARG* 2.9 46.2 + - - +
66A LEU* 4.6 3.7 + - + -
67A PRO 3.9 0.4 - - - -
68A ASN* 1.3 70.6 - - - +
70A ARG* 1.3 60.2 + - - +
71A ILE 2.8 29.1 + - - -
72A TYR* 3.0 22.7 + - + +
73A THR 5.4 0.7 + - - -
81A ASN* 3.5 24.2 + - - -
82A ALA 3.1 21.6 + - - +
84A ARG* 2.9 29.3 + - + +
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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