Contacts of the strand formed by residues 100 - 109 (chain A) in PDB entry 1XI1
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.9 22.9 - - + -
64A LYS* 3.4 55.1 - - + +
67A GLY* 3.5 37.2 - - - -
68A ALA* 3.8 9.4 - - + -
71A ILE* 4.0 16.2 - - + -
92A THR* 6.1 0.7 - - + -
93A ILE 3.8 3.8 - - - -
94A ILE* 3.9 35.6 - - + +
98A GLY* 3.3 17.1 + - - -
99A GLN* 1.3 73.6 - - - +
101A TYR* 1.3 60.5 + - - +
102A MET 5.2 0.9 - - - +
103A ILE* 4.1 11.2 - - + -
121A ASP* 3.7 9.4 - - - +
124A LYS* 2.9 27.2 + - - +
412A LEU* 4.8 0.9 - - + -
414A PHE* 3.9 27.9 - + - -
560A GLN* 5.0 3.1 - - - -
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Residues in contact with TYR 101 (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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63A LEU* 4.1 4.9 - - - -
93A ILE* 2.8 32.4 + - + +
95A SER* 4.5 9.4 - - - -
99A GLN* 3.4 46.7 + - + -
100A TRP* 1.3 75.1 - - - +
102A MET* 1.3 66.1 + - - +
120A TYR* 3.8 21.5 - - - -
121A ASP* 3.9 6.6 + - - -
124A LYS* 3.7 31.7 - - + +
188A MET* 4.0 31.0 - - + +
189A THR* 4.7 11.0 - - + -
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Residues in contact with MET 102 (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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63A LEU* 4.0 3.8 - - - +
91A ASN* 4.0 15.5 - - - +
92A THR* 3.3 9.6 - - - -
93A ILE* 3.0 63.1 + - + +
94A ILE* 5.4 1.0 - - - +
100A TRP* 3.9 2.1 - - - +
101A TYR* 1.3 83.2 - - + +
103A ILE* 1.3 69.2 + - - +
104A ASP* 4.0 21.3 - - + +
118A VAL* 3.5 31.0 - - + -
119A ILE 3.2 7.4 - - - +
120A TYR* 4.3 13.5 - - + -
188A MET* 4.8 4.5 - - - +
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Residues in contact with ILE 103 (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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63A LEU* 3.8 19.3 - - + -
67A GLY* 3.8 29.2 - - - +
70A ILE* 4.2 10.3 - - + -
71A ILE* 3.8 31.4 - - + -
74A LEU* 4.5 6.7 - - + -
90A TYR* 4.5 3.1 - - + -
91A ASN 3.7 8.1 - - - +
92A THR* 4.6 2.9 - - + -
100A TRP* 4.1 9.4 - - + -
102A MET* 1.3 79.4 - - - +
104A ASP* 1.3 60.3 + - - +
105A ILE* 4.2 19.7 - - + +
117A THR 3.8 2.4 - - - +
118A VAL* 3.4 1.6 - - - -
119A ILE* 2.7 48.3 + - + +
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Residues in contact with ASP 104 (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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90A TYR* 3.0 6.2 - - - +
91A ASN* 2.9 46.5 + - + +
102A MET* 4.0 22.4 - - + +
103A ILE* 1.3 72.1 - - - +
105A ILE* 1.3 66.2 + - - +
106A CYS* 4.0 2.9 + - - +
114A LYS* 4.9 4.7 + - - -
116A HIS* 2.6 36.3 + - - -
117A THR 4.0 1.1 - - - -
118A VAL* 3.1 17.7 - - + +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A MET* 5.9 0.4 - - - -
51A VAL* 4.1 26.0 - - + -
52A LEU* 4.2 14.6 - - + -
70A ILE* 4.8 2.7 - - + -
74A LEU* 3.9 28.5 - - + -
79A PHE* 3.6 30.1 - - + -
89A THR 4.0 1.6 - - - -
90A TYR* 4.2 1.6 - - + -
103A ILE* 4.2 12.8 - - + +
104A ASP* 1.3 76.8 + - - +
106A CYS* 1.3 57.0 + - - +
107A LEU* 5.0 5.0 - - + +
116A HIS* 2.6 33.0 - - - +
117A THR* 3.0 25.2 + - - +
119A ILE* 4.3 14.8 - - + -
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Residues in contact with CYS 106 (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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79A PHE* 3.4 12.8 - - - -
85A GLY* 4.6 15.0 - - - +
86A LEU 4.2 12.6 - - - +
87A PRO* 4.3 8.5 - - - -
88A ASN 3.2 16.3 + - - -
89A THR* 2.9 21.9 + - - +
90A TYR* 5.6 0.2 - - - -
104A ASP* 4.0 3.7 + - - +
105A ILE* 1.3 75.0 - - - +
107A LEU* 1.3 63.4 + - - +
108A GLY* 3.5 22.9 - - - -
109A TYR* 5.1 6.1 - - - -
114A LYS* 4.9 13.0 - - - -
115A ILE 4.7 1.6 - - - -
116A HIS* 4.0 8.3 - - + +
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Residues in contact with LEU 107 (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 LEU* 3.0 48.0 - - + +
79A PHE* 3.9 24.5 - - + -
87A PRO* 4.2 6.0 - - - +
88A ASN* 4.1 14.8 - - - +
105A ILE* 5.0 4.3 - - + +
106A CYS* 1.3 75.0 - - - +
108A GLY* 1.3 61.8 + - - +
109A TYR 4.9 1.2 - - - +
115A ILE* 3.0 40.3 + - + +
116A HIS* 4.9 6.1 - - - -
117A THR* 5.6 1.6 - - - +
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Residues in contact with GLY 108 (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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87A PRO* 3.5 25.8 - - - +
106A CYS* 3.5 10.1 - - - -
107A LEU* 1.3 81.7 - - - +
109A TYR* 1.3 65.6 + - - -
114A LYS* 3.2 7.6 - - - +
115A ILE* 2.7 30.8 + - - +
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Residues in contact with TYR 109 (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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85A GLY* 5.7 5.2 - - - -
86A LEU 5.7 3.1 - - - -
87A PRO* 5.6 8.3 - - + -
106A CYS* 5.1 7.4 - - - -
107A LEU 4.9 1.2 - - - +
108A GLY* 1.3 83.4 - - - -
110A LYS* 1.3 64.7 + - - +
112A LYS* 3.9 14.8 - - - +
113A ARG 3.2 17.7 - - - +
114A LYS* 3.3 42.9 - - + +
115A ILE* 4.1 6.6 - - - +
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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