Contacts of the strand formed by residues 57 - 69 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52G TYR* 3.9 2.6 - - - -
53G LEU* 4.7 1.3 - - - -
54G LEU* 2.9 34.5 + - - +
55G ALA 3.0 2.3 - - - -
56G PRO* 1.3 81.7 - - - +
58G SER* 1.3 60.6 + - - -
91G HIS* 3.5 12.1 - - - -
92G SER 3.4 11.2 - - - -
93G GLY* 3.6 6.7 - - - -
94G VAL 5.1 0.2 - - - -
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Residues in contact with SER 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G TYR* 3.4 14.6 - - - -
53G LEU* 3.7 21.9 - - - +
57G GLY* 1.3 73.5 - - - -
59G GLY* 1.3 58.5 + - - +
91G HIS* 3.6 1.6 + - - -
92G SER* 2.9 38.3 + - - -
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Residues in contact with GLY 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G ARG* 3.6 1.0 - - - +
52G TYR* 2.9 51.7 + - - +
58G SER* 1.3 76.3 - - - +
60G THR* 1.3 67.3 + - - -
90G GLY 3.1 13.2 - - - -
91G HIS* 4.2 0.2 - - - -
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Residues in contact with THR 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G GLU* 3.6 24.0 - - + +
50G PHE 3.5 8.1 - - - +
51G ARG* 4.0 17.0 - - + +
52G TYR* 4.1 0.6 - - - -
59G GLY* 1.3 76.3 + - - -
61G MET* 1.3 73.2 + - - +
88G TYR* 3.5 14.2 - - + -
89G TRP* 3.5 0.5 - - - -
90G GLY* 2.9 37.9 + - - -
121G TYR* 3.7 13.9 - - + +
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Residues in contact with MET 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G GLU* 3.6 1.6 - - - -
50G PHE* 2.9 56.1 + - + +
52G TYR* 4.2 10.8 - - + -
60G THR* 1.3 77.5 - - - +
62G ALA* 1.3 64.3 + - - +
87G TYR* 3.2 33.7 - - + +
88G TYR 3.3 5.8 - - - +
89G TRP* 3.4 38.1 - - + +
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Residues in contact with ALA 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ASN 3.2 12.3 - - - +
49G GLU* 4.6 3.6 - - + -
61G MET* 1.3 78.1 - - - +
63G LEU* 1.3 62.2 + - - +
64G ASP* 4.3 4.9 - - - +
86G LEU* 3.6 3.0 - - + +
87G TYR* 3.4 9.0 - - - -
88G TYR* 2.9 38.3 + - + +
121G TYR* 3.5 37.0 - - + +
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Residues in contact with LEU 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ASN* 2.9 61.1 + - + +
62G ALA* 1.3 73.9 - - - +
64G ASP* 1.3 73.2 + - - +
65G TRP* 5.0 7.0 - - + -
85G TRP* 4.9 8.7 - - + -
86G LEU 3.2 19.3 - - - +
87G TYR* 4.5 18.4 - - + -
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Residues in contact with ASP 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G GLN* 4.2 7.5 + - - +
46G TRP 3.3 4.3 - - - +
47G GLN* 3.5 39.9 + - - +
48G ASN 4.1 2.8 + - - +
62G ALA* 5.0 3.1 - - - +
63G LEU* 1.3 82.8 + - - +
65G TRP* 1.3 61.3 + - - +
66G LEU 4.4 0.2 - - - -
84G ARG 4.5 0.2 - - - -
85G TRP* 3.1 9.7 - - - +
86G LEU* 2.9 43.0 + - + +
113G TYR* 3.4 25.1 + - - +
118G THR 4.8 0.5 - - - +
119G SER* 4.5 14.2 - - - -
121G TYR* 5.9 1.7 - - - -
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Residues in contact with TRP 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G GLN* 4.0 1.7 - - - +
46G TRP* 2.9 60.2 + + + +
48G ASN* 5.3 3.6 - - - +
63G LEU* 5.0 11.2 - - + +
64G ASP* 1.3 74.5 - - - +
66G LEU* 1.3 59.4 + - - +
67G PRO* 3.5 38.5 - - + +
83G THR* 3.3 30.1 - - + +
84G ARG 3.6 2.2 - - - -
85G TRP* 4.6 8.1 - + + -
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Residues in contact with LEU 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G MET* 4.1 9.4 - - + -
42G ARG* 3.7 23.1 - - + +
43G GLY* 3.7 10.3 - - - -
44G LEU 3.2 40.8 - - - +
45G GLN* 3.6 15.2 - - + +
65G TRP* 1.3 72.0 - - - +
67G PRO* 1.3 66.3 - - + +
68G ASN 5.0 0.7 - - - +
69G ASP* 3.7 31.4 - - + +
82G ALA 3.8 1.4 - - - +
83G THR* 3.3 3.4 - - - -
84G ARG* 2.8 49.9 + - + +
117G LEU* 4.1 6.3 - - + -
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Residues in contact with PRO 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LEU* 3.2 22.4 - - + +
46G TRP* 4.7 4.0 - - + +
65G TRP* 3.5 43.3 - - + +
66G LEU* 1.3 86.0 - - + +
68G ASN* 1.3 79.5 + - - +
81G ASN 4.3 1.9 - - - +
82G ALA 3.1 14.7 - - - +
83G THR* 3.3 22.5 + - + +
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Residues in contact with ASN 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ARG 4.3 2.1 - - - +
43G GLY* 5.8 1.6 - - - -
66G LEU* 5.0 2.1 - - - +
67G PRO* 1.3 95.8 - - - +
69G ASP* 1.3 67.4 + - - +
70G ARG* 3.2 16.0 + - + +
81G ASN* 3.6 27.8 + - + +
82G ALA 4.0 1.8 - - - -
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Residues in contact with ASP 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ARG* 3.0 42.3 + - - +
66G LEU* 4.2 8.7 + - + +
67G PRO 3.7 0.4 - - - -
68G ASN* 1.3 74.9 - - - +
70G ARG* 1.3 59.9 + - - +
71G ILE 2.8 30.3 + - - -
72G TYR* 2.9 19.4 + - + +
80G LYS 3.8 5.2 - - - +
81G ASN* 3.5 18.7 - - - -
82G ALA 3.3 19.8 + - - +
84G ARG* 2.9 35.5 + - + +
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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