Contacts of the strand formed by residues 99 - 108 (chain A) in PDB entry 5IXM
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A VAL* 3.1 10.0 - - - +
95A MET* 2.9 60.2 + - + +
96A ASP* 4.1 10.3 + - + +
98A VAL* 1.3 97.1 - - + +
100A ARG* 1.3 59.8 + - - +
101A PHE* 3.9 27.6 - + + -
136A GLY 3.6 13.7 - - - -
137A TYR* 3.9 32.8 - + + -
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Residues in contact with ARG 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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93A GLY 3.6 5.2 - - - +
94A VAL* 3.6 18.4 - - + +
97A GLN 4.8 2.8 + - - -
98A VAL 4.2 7.4 - - - +
99A TRP* 1.3 80.2 - - - +
101A PHE* 1.3 64.5 + - - +
102A ASN* 4.9 11.8 - - - +
134A THR* 3.7 3.6 - - + +
135A ALA* 3.3 5.9 - - - -
136A GLY* 2.9 46.4 + - - +
137A TYR 5.1 0.9 - - - -
138A ALA* 3.9 22.3 - - - +
145A THR* 6.0 2.0 - - - -
23B ASP* 2.8 42.4 + - - -
25B TYR 4.3 3.0 - - - -
26B GLY* 3.8 13.4 - - - +
27B PRO* 3.9 18.5 - - - +
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Residues in contact with PHE 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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56A PRO* 3.7 28.5 - - + +
91A HIS* 3.8 18.8 - - + +
92A SER* 3.4 2.3 - - - -
93A GLY 2.9 29.2 + - - +
95A MET* 3.6 34.5 - - + -
99A TRP* 3.9 23.8 - + + -
100A ARG* 1.3 81.0 - - - +
102A ASN* 1.3 73.8 + - - +
103A ILE* 6.2 0.9 - - + -
134A THR 3.4 2.0 - - - +
135A ALA* 3.8 24.5 - - + -
136A GLY 5.1 1.1 - - - -
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Residues in contact with ASN 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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91A HIS 3.4 4.2 - - - +
92A SER* 3.7 17.8 - - - -
93A GLY 4.2 2.0 + - - +
100A ARG* 4.9 11.3 - - - +
101A PHE* 1.3 89.4 + - - +
103A ILE* 1.3 65.8 + - - +
132A ILE* 4.0 3.1 - - + +
133A PHE* 3.7 1.4 - - - -
134A THR* 2.9 58.3 + - - +
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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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89A TRP* 3.4 59.5 - - + +
90A GLY* 3.2 5.5 - - - -
91A HIS* 2.9 48.4 + - + +
101A PHE* 6.2 1.3 - - + -
102A ASN* 1.3 80.8 - - - +
104A ASN* 1.3 63.7 + - - +
105A TYR* 4.1 5.4 - - + +
132A ILE 3.5 3.6 - - - +
133A PHE* 3.6 37.2 - - + -
134A THR 5.2 0.9 - - - +
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Residues in contact with ASN 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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88A TYR* 4.5 15.2 + - - -
89A TRP 3.8 1.8 - - - -
90A GLY* 4.9 0.4 - - - -
102A ASN 4.3 0.2 - - - -
103A ILE* 1.3 74.4 - - - +
105A TYR* 1.3 59.4 + - - +
106A THR* 4.9 2.9 + - - -
130A THR* 2.9 41.8 + - - +
132A ILE* 2.9 40.8 + - + +
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Residues in contact with TYR 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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87A TYR* 3.6 36.8 - + - -
88A TYR* 3.4 4.2 - - - -
89A TRP* 2.9 44.9 + - + +
103A ILE* 4.2 4.3 - - + -
104A ASN* 1.3 74.8 + - - +
106A THR* 1.3 68.8 + - - +
107A ARG* 3.6 41.7 + - + -
130A THR 3.5 0.7 - - - -
131A GLN* 3.6 30.6 + - + -
133A PHE* 3.4 42.6 - + + -
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Residues in contact with THR 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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86A LEU* 4.7 6.7 - - + -
87A TYR 3.5 7.6 - - - +
88A TYR* 3.2 20.6 - - + -
104A ASN* 4.9 2.9 + - - -
105A TYR* 1.3 81.8 + - - +
107A ARG* 1.3 66.3 + - - +
114A PHE* 4.3 12.8 - - + -
121A TYR* 4.1 20.0 + - + +
129A ALA* 3.4 27.1 - - + +
130A THR 2.9 14.9 + - - -
131A GLN* 3.2 21.7 + - - +
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Residues in contact with ARG 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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85A TRP* 3.6 34.6 - - + -
86A LEU* 3.5 2.4 - - - +
87A TYR* 2.9 36.4 + - + +
105A TYR* 3.6 28.0 + - + -
106A THR* 1.3 76.9 - - - +
108A VAL* 1.3 68.3 + - - +
129A ALA* 4.9 0.2 - - - -
131A GLN* 3.7 10.7 - - - +
152A GLN* 3.4 16.1 - - - +
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Residues in contact with VAL 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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85A TRP* 3.5 16.6 - - - +
86A LEU* 3.6 30.7 - - + -
106A THR* 4.7 2.7 - - + -
107A ARG* 1.3 78.8 + - - +
109A SER* 1.3 60.9 + - - +
110A ASP 3.4 18.8 - - - +
113A TYR* 3.9 18.6 - - + -
114A PHE* 3.6 17.5 - - + -
129A ALA* 5.3 1.1 - - + -
152A GLN* 2.8 30.7 + - - +
154A PHE* 3.7 28.0 - - + -
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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