Contacts of the strand formed by residues 99 - 108 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C VAL* 3.1 10.7 - - - +
95C MET* 2.9 62.6 + - + +
96C ASP* 4.2 11.3 + - + +
98C VAL* 1.3 94.5 - - + +
100C ARG* 1.3 59.8 + - - +
101C PHE* 3.9 27.1 - + + -
136C GLY 3.6 13.2 - - - -
137C TYR* 3.9 32.8 - + + -
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C GLY 3.6 5.4 - - - +
94C VAL* 3.8 19.6 - - + +
97C GLN 4.6 4.2 + - - -
98C VAL 4.0 7.2 - - - +
99C TRP* 1.3 79.8 - - - +
101C PHE* 1.3 65.3 + - - +
102C ASN* 5.0 10.1 - - - +
134C THR* 3.7 3.4 - - + +
135C ALA* 3.3 5.7 - - - -
136C GLY* 2.9 46.1 + - - +
137C TYR 5.0 1.3 - - - -
138C ALA* 3.9 21.1 - - - +
145C THR* 5.9 2.2 - - - -
23D ASP* 2.7 43.4 + - - -
25D TYR* 4.1 4.2 - - - +
26D GLY* 3.6 20.9 - - - +
27D PRO* 3.8 13.1 - - - +
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Residues in contact with PHE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C PRO* 3.7 28.9 - - + +
91C HIS* 3.8 12.1 - - + -
92C SER* 3.4 2.3 - - - -
93C GLY 2.9 30.2 + - - +
95C MET* 3.8 29.2 - - + -
99C TRP* 3.9 25.6 - + + -
100C ARG* 1.3 80.2 - - - +
102C ASN* 1.3 74.5 + - - +
134C THR 3.5 2.2 - - - +
135C ALA* 3.7 25.1 - - + -
136C GLY 5.1 1.1 - - - -
604C C8E 3.5 26.9 - - - +
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Residues in contact with ASN 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C HIS 3.3 4.4 - - - +
92C SER* 3.6 20.8 + - - -
93C GLY 4.2 1.1 + - - +
100C ARG* 5.0 9.3 - - - +
101C PHE* 1.3 88.1 + - - +
103C ILE* 1.3 65.6 + - - +
132C ILE* 4.0 1.7 - - + +
133C PHE* 3.7 0.9 - - - -
134C THR* 2.9 60.4 + - - +
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Residues in contact with ILE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C TRP* 3.4 61.0 - - + +
90C GLY* 3.2 5.0 - - - -
91C HIS* 2.9 42.4 + - + +
102C ASN* 1.3 80.4 - - - +
104C ASN* 1.3 64.7 + - - +
105C TYR* 4.0 6.1 - - + +
132C ILE 3.5 2.9 - - - +
133C PHE* 3.7 36.6 - - + -
134C THR 5.2 0.7 - - - +
604C C8E 3.6 21.5 - - - -
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Residues in contact with ASN 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C TYR* 4.3 17.0 + - - -
89C TRP 3.8 1.6 - - - -
90C GLY* 4.8 0.4 - - - -
102C ASN 4.3 0.2 - - - -
103C ILE* 1.3 73.4 - - - +
105C TYR* 1.3 59.6 + - - +
106C THR* 5.0 2.3 + - - -
130C THR* 3.0 40.2 - - - +
132C ILE* 2.9 39.4 + - + +
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Residues in contact with TYR 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C TYR* 3.5 40.4 - + - -
88C TYR* 3.3 4.3 - - - -
89C TRP* 2.9 45.0 + + + +
103C ILE* 4.1 11.7 - - + -
104C ASN* 1.3 74.4 + - - +
106C THR* 1.3 68.3 + - - +
107C ARG* 3.7 39.2 + - + -
130C THR 3.5 0.7 - - - -
131C GLN* 3.5 34.6 + - + -
133C PHE* 3.6 30.5 - + + -
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Residues in contact with THR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C LEU* 4.7 7.0 - - + -
87C TYR 3.4 7.9 - - - +
88C TYR* 3.2 19.6 - - + -
104C ASN* 5.0 2.4 + - - -
105C TYR* 1.3 80.6 + - - +
107C ARG* 1.3 67.0 + - - +
114C PHE* 4.3 12.8 - - + -
121C TYR* 3.9 23.0 + - + +
129C ALA* 3.4 27.0 - - + +
130C THR 2.9 13.9 + - - -
131C GLN* 3.3 21.0 + - - +
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Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C TRP* 3.7 31.4 - - + -
86C LEU* 3.5 2.4 - - - +
87C TYR* 2.9 36.4 + - + +
105C TYR* 3.7 27.8 + - + -
106C THR* 1.3 76.7 - - - +
108C VAL* 1.3 71.8 + - - +
131C GLN* 3.7 11.6 - - - +
152C GLN* 3.3 15.8 - - - +
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Residues in contact with VAL 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C TRP* 3.5 15.7 - - - +
86C LEU* 3.6 17.9 - - + -
106C THR* 4.8 2.7 - - + -
107C ARG* 1.3 80.1 + - - +
109C SER* 1.3 61.1 + - - +
110C ASP 3.3 19.3 - - - +
113C TYR* 3.9 19.7 - - + -
114C PHE* 3.6 30.7 - - + -
129C ALA* 5.4 0.4 - - + -
152C GLN* 2.8 38.9 + - - +
154C PHE* 3.9 17.5 - - + -
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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