Contacts of the helix formed by residues 106 - 121 (chain M) in PDB entry 5XTD
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 SER 106 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81M GLU* 2.7 25.4 + - - +
103M LEU* 3.0 38.8 + - - +
104M THR 3.2 0.4 - - - +
105M ASN* 1.3 81.7 - - - +
107M GLU* 1.3 68.3 + - - +
108M LYS* 3.3 1.8 + - - +
109M SER* 3.2 14.9 + - - -
110M LYS* 3.4 8.5 + - - +
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Residues in contact with GLU 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I CYS* 5.0 12.5 - - + +
105M ASN 3.7 2.1 + - - -
106M SER* 1.3 76.6 + - - +
108M LYS* 1.3 72.9 + - - +
110M LYS* 3.0 28.0 + - - +
111M LYS* 2.9 58.9 + - - +
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Residues in contact with LYS 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A HIS* 5.5 0.5 + - - -
81M GLU* 3.2 28.3 + - + +
85M ALA 4.0 7.1 + - - -
86M PRO 3.1 28.3 + - - -
87M LYS* 3.3 15.7 - - - +
88M VAL* 3.8 20.9 - - + +
106M SER* 3.2 2.2 + - - +
107M GLU* 1.3 88.5 + - - +
109M SER* 1.3 57.9 + - - +
111M LYS* 3.1 13.0 + - + +
112M ALA* 2.9 26.0 + - - +
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Residues in contact with SER 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M LEU 3.1 16.5 + - - -
80M VAL* 3.4 16.6 - - - +
81M GLU* 2.9 19.7 + - - -
88M VAL* 4.9 0.4 - - - -
103M LEU 4.6 2.7 - - - -
104M THR 3.8 8.0 + - - -
106M SER 3.2 11.3 + - - -
108M LYS* 1.3 75.4 - - - +
110M LYS* 1.3 57.5 + - - +
112M ALA* 3.1 10.6 + - - +
113M ARG* 2.7 56.6 + - - +
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Residues in contact with LYS 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I TYR* 5.3 8.3 - - + -
55I CYS* 3.2 44.0 + - - +
58I ASP* 4.5 5.5 + - - -
61I ARG* 6.2 3.1 - - - +
105M ASN 5.5 3.8 + - - +
106M SER 3.4 6.3 + - - +
107M GLU* 3.0 24.4 + - - +
109M SER* 1.3 78.2 - - - +
111M LYS* 1.3 59.9 + - - +
113M ARG* 3.2 14.3 + - - +
114M GLU* 2.9 48.9 + - + +
146M PHE* 4.7 17.3 - - + -
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Residues in contact with LYS 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A LYS* 5.9 8.3 - - + +
418A GLN* 4.3 5.7 + - + -
422A HIS* 4.3 9.0 - - + +
53I TYR* 3.2 48.9 - - + +
55I CYS* 5.6 2.2 - - - -
107M GLU* 2.9 36.5 + - - +
108M LYS* 3.1 15.5 + - + +
110M LYS* 1.3 76.6 - - - +
112M ALA* 1.3 57.5 + - - +
114M GLU* 3.5 13.9 + - - +
115M GLY* 2.9 23.2 + - - -
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Residues in contact with ALA 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A HIS* 3.8 20.6 + - + +
79M LEU* 3.6 36.9 - - + +
88M VAL* 4.7 4.5 - - + -
108M LYS 2.9 12.8 + - - +
109M SER* 3.2 13.5 - - - +
111M LYS* 1.3 75.3 - - - +
113M ARG* 1.3 60.4 + - - +
115M GLY* 2.7 18.2 + - - -
116M VAL* 2.9 16.9 + - - +
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Residues in contact with ARG 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58M MET* 4.8 7.2 - - - +
60M ILE* 4.8 4.8 - - - +
61M PRO* 3.1 43.7 - - - +
77M MET* 3.7 34.6 + - + +
79M LEU* 4.6 4.5 - - - +
80M VAL* 4.1 12.7 - - - +
104M THR* 3.6 24.7 + - - -
109M SER* 2.7 48.8 + - - +
110M LYS* 3.2 10.9 + - - +
112M ALA* 1.3 75.4 - - + +
114M GLU* 1.3 58.5 + - - +
116M VAL* 3.0 4.9 + - - +
117M MET* 2.9 30.4 + - - +
146M PHE* 3.8 37.2 - - + -
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Residues in contact with GLU 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLN* 3.6 8.1 - - - +
53I TYR* 3.1 30.9 - - + +
54I TYR* 3.5 26.4 + - + +
55I CYS* 4.1 5.2 + - - +
110M LYS* 2.9 40.6 + - + +
111M LYS* 3.5 14.9 + - - +
112M ALA 3.1 0.2 - - - -
113M ARG* 1.3 76.1 - - + +
115M GLY* 1.3 58.4 + - - +
118M GLU* 3.0 38.5 + - + +
146M PHE* 5.6 1.6 - - + -
147M GLY* 4.2 26.7 - - - +
148M ASN* 4.3 8.5 - - - +
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Residues in contact with GLY 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A PRO* 5.9 1.1 - - - -
418A GLN* 3.3 31.4 - - - -
422A HIS* 4.6 5.4 - - - -
111M LYS 2.9 8.7 + - - -
112M ALA 2.7 10.9 + - - -
114M GLU* 1.3 78.4 - - - +
116M VAL* 1.3 58.5 + - - -
119M PHE* 2.9 34.4 + - - -
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Residues in contact with VAL 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A THR* 4.6 13.4 - - + +
384A PRO* 5.8 6.3 - - + -
63M PHE* 4.3 4.0 - - + -
75M CYS* 5.1 0.9 - - - -
76M ARG* 3.2 29.6 - - + +
77M MET* 3.6 29.4 - - + +
79M LEU* 4.7 4.0 - - + -
112M ALA 2.9 17.0 + - - +
113M ARG* 3.0 6.9 + - - +
115M GLY* 1.3 77.4 - - - +
117M MET* 1.3 59.6 + - - +
119M PHE* 3.0 22.5 + - - +
120M LEU* 3.0 37.5 + - + +
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Residues in contact with MET 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M PHE* 4.2 21.1 - - + -
77M MET* 4.8 7.9 - - + -
113M ARG 2.9 14.8 + - - +
116M VAL* 1.3 75.5 - - - +
118M GLU* 1.3 65.9 - - - +
119M PHE 3.2 0.7 + - - -
120M LEU* 4.4 9.6 - - - +
121M LEU* 3.4 54.7 + - + +
139M LEU* 4.2 8.5 - - + +
142M GLN* 3.2 36.8 - - + +
143M SER* 3.5 9.0 - - - +
146M PHE* 3.6 15.7 - - + +
147M GLY* 3.9 17.0 - - - +
376Q GLU* 4.1 2.8 - - - +
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Residues in contact with GLU 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A GLU* 5.5 0.2 - - - +
418A GLN* 3.9 25.8 - - - +
114M GLU* 3.0 26.6 + - + +
116M VAL 3.2 0.2 - - - -
117M MET* 1.3 77.1 - - - +
119M PHE* 1.3 66.9 + - + +
121M LEU* 4.1 1.7 - - - +
122M ALA* 3.4 20.6 + - - +
147M GLY 4.1 0.5 - - - -
148M ASN* 3.1 49.3 + - - +
150M ARG 4.4 6.9 - - - +
151M SER* 4.9 2.6 - - - -
152M ARG* 4.4 25.2 + - - +
376Q GLU* 3.7 15.2 - - - +
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Residues in contact with PHE 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A THR* 4.8 5.6 - - + +
384A PRO* 3.8 33.7 - - + -
387A GLU* 3.1 42.5 - - + +
388A GLY* 5.1 4.3 - - - -
391A TRP* 5.5 5.6 - + - -
415A ILE* 4.1 31.6 - - + -
418A GLN* 3.1 53.6 - - + -
419A ILE* 4.7 2.5 - - + -
115M GLY 2.9 17.3 - - - -
116M VAL* 3.0 7.2 + - - +
118M GLU* 1.3 84.5 - - + +
120M LEU* 1.3 68.0 + - - +
121M LEU 3.1 1.8 - - - -
122M ALA* 3.0 12.9 + - + +
152M ARG* 5.5 1.8 - - - -
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Residues in contact with LEU 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A THR* 3.4 35.4 - - + +
386A ARG* 5.3 2.0 - - - +
387A GLU* 5.6 0.3 - - - -
63M PHE* 3.7 38.4 - - + -
75M CYS* 4.9 4.5 - - - -
116M VAL* 3.0 32.0 + - + +
117M MET* 3.6 11.2 + - - +
119M PHE* 1.3 77.1 - - - +
121M LEU* 1.3 67.2 + - + +
122M ALA 3.3 0.6 + - - -
123M ASN* 4.1 1.6 + - - +
124M HIS* 3.7 18.7 + - - +
139M LEU* 4.9 12.9 - - + +
177M ILE* 4.8 22.4 - - + +
178M GLN* 6.0 0.4 - - - +
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Residues in contact with LEU 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M MET* 3.4 38.4 + - + +
118M GLU 4.1 1.8 - - - +
119M PHE 3.1 0.6 - - - -
120M LEU* 1.3 78.1 - - - +
122M ALA* 1.3 64.0 + - - +
123M ASN 3.1 4.2 + - - -
124M HIS* 3.7 21.5 + - + -
139M LEU* 3.6 30.3 - - + -
143M SER* 3.9 4.9 - - - +
151M SER* 5.8 3.8 - - - -
153M PHE* 5.9 0.7 - - - +
157M LYS* 3.9 10.6 + - - -
375Q MET* 4.2 11.1 - - + +
376Q GLU* 3.5 41.7 - - + +
379Q ILE* 3.8 20.0 - - + -
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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