Contacts of the strand formed by residues 99 - 108 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94G VAL* 3.2 9.9 - - - +
95G MET* 2.9 62.0 + - + +
96G ASP* 4.0 13.6 + - + +
98G VAL* 1.3 95.7 - - + +
100G ARG* 1.3 60.6 + - - +
101G PHE* 4.0 26.0 - + + -
136G GLY 3.6 13.0 - - - -
137G TYR* 4.0 32.8 - + + -
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Residues in contact with ARG 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G GLY 3.6 5.2 - - - +
94G VAL* 3.7 18.2 - - + +
97G GLN 4.8 3.6 + - - +
98G VAL 4.1 7.6 - - - +
99G TRP* 1.3 78.8 - - - +
101G PHE* 1.3 64.0 + - - +
102G ASN* 5.0 14.2 - - - +
134G THR* 3.7 3.4 - - + +
135G ALA* 3.3 6.4 - - - -
136G GLY* 2.9 46.8 + - - +
137G TYR 5.1 1.1 - - - -
138G ALA* 3.8 22.4 - - - -
145G THR* 5.9 2.2 - - - -
23H ASP* 2.8 43.4 + - - -
25H TYR* 4.2 3.8 - - - +
26H GLY* 3.8 20.4 - - - +
27H PRO* 4.0 12.1 - - - +
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Residues in contact with PHE 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G PRO* 3.8 25.1 - - + -
91G HIS* 3.9 20.2 - - + +
92G SER* 3.4 2.3 - - - -
93G GLY 2.9 30.7 + - - +
95G MET* 3.7 33.0 - - + -
99G TRP* 4.0 23.3 - + + -
100G ARG* 1.3 80.8 - - - +
102G ASN* 1.3 74.0 + - - +
103G ILE* 6.0 1.1 - - + -
134G THR 3.4 2.9 - - - +
135G ALA* 3.7 26.7 - - + -
136G GLY 5.1 0.9 - - - -
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Residues in contact with ASN 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G HIS 3.3 4.7 - - - +
92G SER* 3.5 21.7 + - - -
93G GLY 4.2 1.1 + - - +
100G ARG* 5.0 13.1 - - - +
101G PHE* 1.3 86.2 - - - +
103G ILE* 1.3 64.2 + - - +
132G ILE* 4.1 2.2 - - - +
133G PHE* 3.7 1.2 - - - -
134G THR* 2.9 57.6 + - + +
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Residues in contact with ILE 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G TRP* 3.3 63.9 - - + +
90G GLY* 3.3 5.0 - - - -
91G HIS* 2.9 51.5 + - + +
101G PHE* 6.0 1.1 - - + -
102G ASN* 1.3 80.8 - - - +
104G ASN* 1.3 65.7 + - - +
105G TYR* 4.0 5.2 - - + +
132G ILE 3.6 2.7 - - - +
133G PHE* 4.0 32.5 - - + -
134G THR 5.2 1.3 - - - +
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Residues in contact with ASN 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G TYR* 4.3 17.8 + - - -
89G TRP 3.8 1.6 - - - -
90G GLY* 4.8 0.7 - - - -
102G ASN 4.4 0.2 - - - -
103G ILE* 1.3 73.0 - - - +
105G TYR* 1.3 59.3 + - - +
106G THR* 4.9 2.8 + - - -
130G THR* 3.1 36.2 - - - +
132G ILE* 2.9 39.7 + - + +
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Residues in contact with TYR 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G TYR* 3.7 36.8 - + - -
88G TYR* 3.3 4.5 - - - -
89G TRP* 2.9 46.0 + + + +
103G ILE* 4.1 5.4 - - + -
104G ASN* 1.3 73.1 + - - +
106G THR* 1.3 68.5 + - - +
107G ARG* 3.5 38.3 + - + -
130G THR 3.6 0.7 - - - -
131G GLN* 3.4 35.9 + - + -
133G PHE* 3.4 43.7 - + + -
150G GLN* 6.0 0.4 - - - -
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Residues in contact with THR 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G LEU* 4.8 5.2 - - + -
87G TYR 3.5 8.5 - - - +
88G TYR* 3.2 20.8 - - + -
104G ASN* 4.9 2.8 + - - -
105G TYR* 1.3 79.8 + - - +
107G ARG* 1.3 67.0 + - - +
108G VAL* 4.8 1.6 - - + -
114G PHE* 4.4 11.7 - - + -
121G TYR* 4.1 19.9 + - + +
129G ALA* 3.5 27.1 - - + +
130G THR 2.9 14.9 + - - +
131G GLN* 3.1 22.3 + - - +
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Residues in contact with ARG 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G TRP* 3.7 30.3 - - + -
86G LEU* 3.5 2.6 - - - +
87G TYR* 2.9 36.4 + - + +
105G TYR* 3.5 29.2 + - + -
106G THR* 1.3 76.7 - - - +
108G VAL* 1.3 70.2 + - - +
129G ALA* 4.9 0.2 - - - -
131G GLN* 3.7 11.0 - - - +
152G GLN* 3.4 14.8 - - - +
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Residues in contact with VAL 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G TRP* 3.5 16.7 - - - +
86G LEU* 3.7 28.5 - - + -
106G THR* 4.8 3.1 - - + -
107G ARG* 1.3 79.4 + - - +
109G SER* 1.3 59.9 + - - +
110G ASP 3.4 18.2 - - - +
113G TYR* 4.0 17.9 - - + -
114G PHE* 3.8 19.7 - - + -
129G ALA* 5.2 0.7 - - + -
152G GLN* 2.8 40.6 + - - +
154G PHE* 3.8 17.9 - - + -
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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