Contacts of the strand formed by residues 99 - 109 (chain A) in PDB entry 5IXG
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 LYS 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ARG* 5.2 4.9 - - - +
95A PHE* 3.2 5.1 - - - -
96A ASP 2.8 34.6 + - - +
97A GLY 3.4 0.8 - - - -
98A ASP* 1.3 85.4 - - + +
100A PRO* 1.3 78.1 - - + +
101A VAL* 3.6 4.1 - - + +
122A SER* 5.8 0.9 - - - +
123A PHE* 3.0 49.6 + - + +
124A LYS* 5.3 0.2 - - - +
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Residues in contact with PRO 100 (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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44A LEU* 4.5 4.7 - - + -
46A ARG* 5.2 0.4 - - - +
93A ILE* 3.8 15.5 - - + -
94A LYS 3.5 6.7 - - - +
95A PHE* 3.7 26.7 - - + -
98A ASP 4.1 0.9 - - - +
99A LYS* 1.3 98.8 - - + +
101A VAL* 1.3 61.0 + - - +
120A ILE* 3.7 34.3 - - + +
123A PHE* 3.8 41.7 - - + +
201A OTP 6.1 0.4 - - + -
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LYS* 2.8 19.4 + - + +
95A PHE 3.8 3.8 - - - +
96A ASP* 2.8 50.9 - - + +
99A LYS* 3.6 6.3 - - + +
100A PRO* 1.3 77.6 - - - +
102A SER* 1.4 72.4 + - - +
119A LYS* 3.8 7.4 - - - +
120A ILE* 2.9 31.0 + - - +
160D LYS* 5.4 7.4 - - - -
162D LYS* 6.1 6.1 - - + -
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Residues in contact with SER 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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93A ILE* 3.4 7.3 - - - +
94A LYS* 2.9 44.0 + - - +
101A VAL* 1.4 84.5 - - - +
103A VAL* 1.3 67.0 + - - +
104A VAL* 4.1 5.5 - - - +
117A THR* 4.3 12.1 - - - +
118A LEU 3.1 16.2 - - - -
119A LYS* 4.4 2.9 - - - -
120A ILE* 3.9 5.2 - - - +
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Residues in contact with VAL 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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53A VAL* 4.2 9.9 - - + -
89A TYR* 3.1 29.3 + - + +
91A GLY 3.6 26.7 - - - +
92A THR 3.3 6.7 - - - +
93A ILE* 4.1 11.0 - - + +
102A SER* 1.3 80.3 - - - +
104A VAL* 1.3 62.0 + - - +
117A THR* 3.2 4.0 - - - +
118A LEU* 2.8 41.0 + - + +
120A ILE* 4.0 11.9 - - + -
201A OTP 3.9 29.4 - - + -
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Residues in contact with VAL 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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89A TYR* 3.8 0.9 - - - -
91A GLY* 3.4 0.3 - - - -
92A THR* 2.9 34.9 + - - +
94A LYS* 4.0 31.9 - - + -
102A SER* 4.1 7.6 - - - +
103A VAL* 1.3 76.6 - - - +
105A GLY* 1.3 62.9 + - - +
117A THR* 3.9 22.7 - - + +
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Residues in contact with GLY 105 (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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89A TYR* 3.3 3.0 + - - -
90A LYS 3.1 14.1 - - - -
91A GLY* 3.7 1.1 - - - -
104A VAL* 1.3 79.2 - - - +
106A ASN* 1.3 76.1 + - - +
115A PRO* 3.4 5.4 - - - +
116A LEU 2.9 32.9 + - - -
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Residues in contact with ASN 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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88A ASN* 3.8 1.0 - - - +
89A TYR* 3.3 9.3 - - - -
90A LYS* 2.9 32.8 + - + +
105A GLY* 1.3 83.7 + - - -
107A LEU* 1.3 60.4 + - - +
108A THR* 5.1 0.9 + - - -
113A THR* 3.9 21.3 - - + +
114A LYS 3.3 7.9 + - - +
115A PRO* 3.6 22.8 - - - +
116A LEU 4.2 0.9 - - - +
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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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87A ALA* 4.5 1.8 - - + -
88A ASN 3.5 15.0 - - - +
89A TYR* 4.0 6.2 - - + -
106A ASN* 1.3 73.2 - - - +
108A THR* 1.3 70.0 + - - +
109A LEU* 4.0 24.2 - - + -
112A VAL 3.4 2.4 - - - +
113A THR* 3.2 1.7 - - - -
114A LYS 2.9 30.0 + - - -
116A LEU* 4.1 28.9 - - + +
144A PHE* 4.6 9.4 - - + -
149A PHE* 3.5 27.5 - - + -
201A OTP 3.8 42.2 - - + -
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Residues in contact with THR 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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86A GLN 4.4 1.8 - - - +
87A ALA* 3.2 9.4 - - - +
88A ASN* 2.7 49.7 + - - -
106A ASN* 5.1 0.9 + - - +
107A LEU* 1.3 72.3 - - - +
109A LEU* 1.3 60.9 + - - +
111A GLY* 4.1 21.1 - - - +
112A VAL 3.3 6.5 - - - +
113A THR* 2.8 28.2 + - - +
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Residues in contact with LEU 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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59A ILE* 4.2 4.7 - - + -
79A PHE* 4.0 20.4 - - + -
86A GLN 5.8 0.2 - - - +
87A ALA* 4.1 9.2 - - + +
107A LEU* 3.9 12.8 - - + -
108A THR* 1.3 74.8 - - - +
110A HIS* 1.3 75.6 + - - +
111A GLY 3.1 1.3 - - - -
112A VAL* 3.0 18.7 + - - +
144A PHE* 3.9 31.4 - - + -
149A PHE* 3.6 26.8 - - + +
151A LEU* 3.9 22.7 - - + -
201A OTP 3.9 31.4 - - + -
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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