Contacts of the strand formed by residues 85 - 96 (chain A) in PDB entry 1X0O
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 TRP 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A GLU 5.0 2.9 - - - -
48A PHE 3.6 3.1 - - - -
49A CYS 3.3 9.0 - - - -
50A HIS* 3.2 51.8 - + + -
51A PRO* 3.8 15.9 - - + -
54A GLN* 5.6 0.7 - - - -
77A ARG* 3.5 38.9 + - + +
78A PHE 3.6 3.8 - - - -
79A ARG* 3.4 51.8 - - + -
83A GLN 3.8 10.7 + - - -
84A GLU* 1.3 78.0 - - - +
86A LEU* 1.3 61.7 + - - +
87A TRP* 5.1 0.3 - - - -
116A SER* 4.2 14.8 + - - +
117A SER* 4.2 5.0 + - - -
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Residues in contact with LEU 86 (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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32A THR 3.9 15.3 - - - +
33A VAL* 3.8 10.3 - - + -
77A ARG* 2.9 4.7 - - - -
78A PHE* 2.8 60.9 + - + +
80A SER* 3.7 26.0 - - - +
84A GLU* 3.8 5.8 - - - +
85A TRP* 1.3 74.3 - - - +
87A TRP* 1.3 61.9 + - - +
88A MET* 4.6 2.9 - - + -
112A ASN* 3.4 22.2 - - - +
114A LYS 3.9 2.9 - - - +
115A ASN* 3.5 35.7 - - - +
116A SER 4.5 2.2 - - - +
117A SER* 4.8 0.2 - - - -
118A GLN* 4.5 4.0 - - - +
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Residues in contact with TRP 87 (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 ASP* 5.0 7.9 - - - -
75A MET* 3.8 37.2 - - + -
76A PHE* 3.6 23.6 - - - -
77A ARG* 3.3 47.0 - - + +
85A TRP 5.1 0.7 - - - -
86A LEU* 1.3 69.9 - - - +
88A MET* 1.3 53.3 + - - +
112A ASN* 3.3 5.9 + - - -
113A VAL* 2.7 33.1 + - - -
114A LYS* 3.0 55.9 + - + +
115A ASN 4.8 0.2 - - - -
116A SER* 4.5 20.6 + - - -
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Residues in contact with MET 88 (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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12A PHE* 3.7 9.2 - - + -
32A THR* 3.6 19.7 - - + -
33A VAL* 3.4 31.9 - - + -
75A MET* 3.6 4.1 - - - +
76A PHE* 2.8 45.1 + - + +
78A PHE* 3.6 32.1 - - + -
86A LEU* 3.4 3.9 + - + +
87A TRP* 1.3 75.3 - - - +
89A ARG* 1.3 65.9 + - - +
110A ASN* 3.4 37.0 - - + +
111A THR 3.5 8.5 - - - +
112A ASN* 3.7 8.7 - - - -
113A VAL* 4.9 0.2 - - - -
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Residues in contact with ARG 89 (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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73A SER* 3.7 27.8 - - - -
74A VAL 3.4 13.9 - - - +
75A MET* 4.2 14.1 - - + +
88A MET* 1.3 73.0 - - - +
90A THR* 1.3 62.1 + - - +
91A SER* 3.8 21.7 + - - -
109A THR 3.5 2.1 - - - +
111A THR* 2.8 57.6 + - - +
113A VAL* 4.4 11.7 - - + +
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Residues in contact with THR 90 (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 ILE* 4.4 1.2 - - - +
61A PHE* 4.5 10.1 - - + -
72A LEU 3.3 3.1 - - - +
73A SER* 3.4 1.2 - - - -
74A VAL* 2.8 46.8 + - - +
76A PHE* 3.0 26.7 - - - -
88A MET* 4.0 0.8 + - - +
89A ARG* 1.3 72.7 - - - +
91A SER* 1.3 72.7 + - - +
92A SER* 4.4 8.1 - - - +
108A CYS* 4.2 19.5 - - - -
109A THR 3.2 4.5 - - - +
110A ASN* 2.8 29.6 + - - +
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Residues in contact with SER 91 (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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71A VAL* 3.6 23.5 - - - +
72A LEU 3.6 4.9 - - - -
73A SER* 4.3 3.8 - - - +
89A ARG* 3.8 27.1 + - - -
90A THR* 1.3 73.6 - - - +
92A SER* 1.3 61.1 + - - +
93A PHE* 3.8 0.9 + - - +
107A ILE 3.3 5.5 - - - +
109A THR* 2.8 49.3 + - - +
111A THR* 5.2 1.2 + - - -
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Residues in contact with SER 92 (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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60A SER* 4.9 2.3 + - - -
61A PHE* 4.1 23.2 - - - -
64A VAL* 3.5 31.6 - - - -
70A GLN 3.3 3.3 - - - +
71A VAL* 3.2 10.9 - - - -
72A LEU* 2.7 42.9 + - - +
74A VAL* 4.1 3.1 - - - +
90A THR* 4.0 7.7 + - - +
91A SER* 1.3 72.9 - - - +
93A PHE* 1.3 60.0 + - - +
106A ILE* 5.1 4.7 - - - -
107A ILE 4.1 2.9 - - - -
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Residues in contact with PHE 93 (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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64A VAL* 4.0 1.8 - - - -
69A GLY* 4.1 26.2 - - - -
70A GLN 4.6 2.7 - - - -
71A VAL* 5.4 5.4 - - + -
91A SER 5.0 1.1 - - - +
92A SER* 1.3 76.0 - - - +
94A THR* 1.3 74.8 + - - +
95A PHE* 3.4 39.9 - + - -
96A GLN 5.0 1.3 - - - -
106A ILE* 3.3 6.7 - - - +
107A ILE* 2.8 64.7 + - + +
109A THR* 5.8 1.3 - - - +
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Residues in contact with THR 94 (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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64A VAL* 3.5 37.4 + - + +
65A VAL* 4.1 8.5 - - + -
68A LYS* 3.3 9.5 - - - +
69A GLY* 3.1 25.1 + - - +
93A PHE* 1.3 90.3 - - - +
95A PHE* 1.3 60.3 + - - +
96A GLN* 3.1 13.3 + - - +
103A ILE* 3.4 28.6 - - + +
105A TYR 4.0 3.4 - - - -
106A ILE* 4.4 9.2 - - + -
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Residues in contact with PHE 95 (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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15A ARG* 5.7 1.6 - - - -
93A PHE* 3.4 27.9 - + + -
94A THR* 1.3 68.7 - - - +
96A GLN* 1.3 72.2 + - - +
97A ASN* 4.7 7.6 - - - -
103A ILE* 3.2 3.7 - - - +
104A GLU* 3.1 58.1 + - + +
105A TYR* 3.1 46.0 + - + +
107A ILE* 3.8 10.5 - - + -
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Residues in contact with GLN 96 (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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68A LYS* 3.1 60.2 - - - +
69A GLY* 3.6 3.3 + - - -
93A PHE* 4.9 2.4 - - - -
94A THR* 3.1 9.1 + - - +
95A PHE* 1.3 84.8 - - - +
97A ASN* 1.3 65.1 + - - +
98A PRO* 3.4 11.2 - - + +
101A ASP* 3.6 26.4 + - - +
102A GLU 3.1 5.6 - - - +
103A ILE* 3.5 20.2 - - + -
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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