Contacts of the strand formed by residues 104 - 113 (chain O) in PDB entry 2AXT
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 LEU 104 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69O LEU 4.8 0.7 - - - -
70O CYS* 3.3 5.6 - - - -
71O LEU* 2.8 51.3 + - + +
102O THR 3.8 2.5 - - - +
103O SER* 1.3 77.2 - - - +
105O ASP* 1.3 64.5 + - - +
107O ILE* 4.3 6.3 - - + -
127O ILE 3.4 9.0 - - - +
128O ASP 4.4 2.7 - - - -
129O PHE 3.9 13.0 - - - +
130O GLN* 4.0 5.8 - - + -
146O PHE* 3.6 48.0 - - + +
147O THR* 4.3 2.7 - - - -
148O VAL* 3.6 41.3 - - + +
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Residues in contact with ASP 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C ARG* 3.8 17.8 - - - +
349C ILE* 5.4 2.0 - - + -
373C ASN* 5.1 4.3 + - - -
45O CYS* 3.9 3.1 - - - +
68O ARG* 2.9 42.2 + - - +
69O LEU 4.1 4.5 - - - -
70O CYS* 3.2 23.1 - - - +
103O SER* 4.1 1.6 + - - -
104O LEU* 1.3 73.5 - - - +
106O GLN* 1.3 98.0 + - - +
107O ILE* 3.0 9.4 + - - +
127O ILE* 2.9 31.4 + - + +
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Residues in contact with GLN 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349C ILE* 4.0 24.1 - - - +
373C ASN* 6.2 1.4 - - - +
375C LEU 4.5 0.3 - - - +
376C ASP* 4.1 11.6 - - - +
377C LEU* 3.6 53.4 + - + +
378C ASN* 5.1 9.2 - - - +
67O ALA 4.7 1.1 - - - +
68O ARG* 4.3 11.2 - - - +
69O LEU 4.2 2.0 + - - -
105O ASP* 1.3 117.6 + - - +
107O ILE* 1.3 64.9 + - - +
108O GLN* 3.3 12.0 + - - +
125O ASP 3.3 9.4 - - - +
126O GLY* 3.6 3.1 - - - -
127O ILE* 4.1 4.4 - - + +
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Residues in contact with ILE 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66O ILE 4.5 0.2 - - - +
68O ARG* 3.5 2.9 - - - -
69O LEU* 2.7 62.9 + - + +
71O LEU* 4.3 7.4 - - + -
104O LEU* 4.3 11.2 - - + -
105O ASP 3.0 13.4 - - - +
106O GLN* 1.3 78.0 - - - +
108O GLN* 1.3 62.9 + - - +
121O PHE* 4.0 4.5 - - + -
123O GLU* 3.6 24.9 - - + +
125O ASP 3.4 5.4 - - - -
126O GLY* 4.1 0.2 - - - -
127O ILE 4.4 0.9 - - - +
128O ASP* 3.8 25.1 - - + +
148O VAL* 3.3 33.9 - - + -
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Residues in contact with GLN 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU* 5.9 1.4 - - - +
378C ASN* 4.6 13.7 + - - +
381C LYS* 3.0 31.9 - - - +
65O ARG* 3.7 23.6 + - - +
66O ILE* 3.4 8.7 - - - +
67O ALA* 3.3 23.6 - - - +
106O GLN 4.0 6.8 + - - +
107O ILE* 1.3 76.2 - - - +
109O GLY* 1.3 53.6 + - - +
121O PHE* 3.9 9.0 - - - -
123O GLU* 3.5 2.8 - - - +
124O GLU* 2.5 32.2 + - + -
125O ASP* 2.9 25.7 + - + +
126O GLY* 5.5 0.4 - - - -
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Residues in contact with GLY 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65O ARG* 3.1 13.1 - - - +
66O ILE 2.9 24.9 + - - -
108O GLN* 1.3 80.0 - - - +
110O GLU* 1.3 61.9 + - - -
121O PHE* 3.6 7.6 - - - -
122O VAL 3.0 16.4 - - - -
124O GLU* 3.6 13.9 - - - -
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Residues in contact with GLU 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63O THR* 5.6 8.3 - - + -
64O TYR 4.2 5.2 - - - +
65O ARG* 3.6 21.0 - - + +
109O GLY* 1.3 71.0 - - - -
111O LEU* 1.3 59.2 + - - +
112O LYS* 3.0 41.0 + - - +
120O THR 3.5 0.3 - - - +
121O PHE* 4.4 0.7 - - - -
122O VAL* 3.1 37.6 + - + +
124O GLU* 5.2 0.2 - - - +
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Residues in contact with LEU 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64O TYR* 2.7 43.5 + - + +
65O ARG* 3.4 4.2 - - - +
66O ILE* 4.1 18.2 - - + -
109O GLY 3.6 0.4 + - - -
110O GLU* 1.3 69.1 - - - +
112O LYS* 1.3 62.1 + - - +
113O VAL* 3.7 4.0 + - - +
119O LEU* 3.7 45.5 - - + -
120O THR 3.6 16.8 - - - -
121O PHE* 3.8 10.1 - - + +
162O ILE* 4.4 2.0 - - + -
168O PHE* 4.1 13.2 - - + -
269O ILE* 3.8 37.5 - - + -
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Residues in contact with LYS 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63O THR* 6.4 1.6 - - - -
110O GLU* 3.0 27.2 + - - +
111O LEU* 1.3 74.4 - - - +
113O VAL* 1.3 62.6 + - - +
114O ASN* 3.8 35.0 + - + +
119O LEU* 3.5 4.5 - - - +
120O THR* 2.8 54.1 + - + +
122O VAL* 4.9 4.5 - - + -
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Residues in contact with VAL 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58O ILE* 5.6 5.2 - - + -
60O SER* 4.2 31.1 - - - +
62O GLN 4.5 4.9 - - - +
63O THR* 5.8 0.2 - - - -
64O TYR* 4.0 25.8 - - + +
111O LEU 3.9 8.3 - - - +
112O LYS* 1.3 76.6 - - - +
114O ASN* 1.3 65.3 + - - +
117O GLY* 4.7 9.6 - - - +
118O SER 4.1 5.4 - - - +
119O LEU* 3.6 26.9 - - + -
159O VAL 5.8 1.6 - - - +
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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