Contacts of the strand formed by residues 84 - 98 (chain C) in PDB entry 1H2I
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 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C PHE* 3.8 4.5 - - - -
72C ILE* 4.1 11.9 - - + -
75C ALA* 3.5 30.5 - - + -
76C ASN* 2.8 25.9 + - - +
79C PHE* 3.9 11.7 - + + -
80C GLY 3.5 16.2 - - - -
81C TYR 4.3 5.7 - - - +
82C ASN 3.6 0.6 - - - -
83C GLY* 1.3 80.2 + - - +
85C ALA* 1.3 75.9 + - - +
86C HIS* 3.6 17.3 - + - -
113C VAL* 4.2 11.0 - - + -
114C GLN 3.1 10.5 - - - +
115C LEU* 3.9 13.5 - - + -
151C LEU* 3.9 26.5 - - + -
155C LEU* 4.2 9.4 - - + -
119D SER* 4.7 3.6 - - - -
121D HIS* 3.3 42.2 + + - -
157D SER* 3.7 22.2 - - - -
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Residues in contact with ALA 85 (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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26C PHE* 3.5 19.5 - - + -
84C TRP* 1.3 81.5 - - - +
86C HIS* 1.3 58.4 + - - +
113C VAL* 3.1 10.0 - - - +
114C GLN 2.7 28.4 + - - +
120D TYR* 2.9 49.8 - - + +
121D HIS* 3.9 3.1 - - - -
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Residues in contact with HIS 86 (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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84C TRP* 3.6 5.3 - + + -
85C ALA* 1.3 78.6 - - - +
87C SER* 1.3 63.5 + - - +
88C ILE* 5.4 0.4 - - + -
111C VAL* 4.1 17.9 - - + -
112C ARG 3.1 11.7 - - - +
113C VAL* 4.1 3.4 - - + -
147C VAL* 5.2 6.2 - - + +
151C LEU* 3.9 38.3 - - + +
120D TYR* 3.1 14.0 + - - -
121D HIS* 2.8 46.8 - + + -
122D GLU* 2.9 47.2 + - - +
123D ASP* 5.0 4.8 + - - -
157D SER* 3.4 19.5 - - - -
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Residues in contact with SER 87 (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 HIS* 1.3 76.1 - - - +
88C ILE* 1.3 64.2 + - - +
89C THR* 3.7 6.1 + - - +
111C VAL* 3.3 7.5 - - - +
112C ARG* 2.9 43.9 + - - +
112D ARG* 5.1 6.3 - - - -
120D TYR* 3.9 18.7 + - - -
122D GLU* 3.5 17.0 - - - -
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Residues in contact with ILE 88 (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 HIS* 5.4 0.9 - - + -
87C SER* 1.3 75.6 - - - +
89C THR* 1.3 62.2 + - - +
90C GLN* 3.7 27.8 - - - +
91C GLN* 4.2 4.5 - - + +
109C ALA* 5.0 3.8 - - + -
110C PHE 3.5 7.4 - - - +
111C VAL* 4.6 6.5 - - + -
147C VAL* 3.8 31.9 - - + -
110D PHE* 3.8 28.3 - - + -
122D GLU* 3.0 32.9 + - + +
123D ASP* 3.8 27.8 - - - -
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Residues in contact with THR 89 (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 SER* 3.7 6.9 + - - +
88C ILE* 1.3 73.6 - - - +
90C GLN* 1.3 64.7 + - - +
110C PHE* 2.8 21.9 + - - +
112C ARG* 4.1 27.4 - - + -
122C GLU* 2.7 30.2 + - - +
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Residues in contact with GLN 90 (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 ILE* 3.1 8.8 - - - +
89C THR* 1.3 86.2 + - - +
91C GLN* 1.3 65.9 + - - +
92C ASN* 3.7 33.1 - - - +
109C ALA* 3.4 1.6 - - - -
110C PHE* 2.8 48.7 + - + -
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Residues in contact with GLN 91 (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 ILE* 4.2 4.8 - - + +
90C GLN* 1.3 80.7 + - - +
92C ASN* 1.3 66.7 + - - +
107C VAL* 3.6 18.8 - - + +
108C CYS 3.3 10.5 - - - +
109C ALA* 3.9 2.3 - - + +
143C ARG* 2.9 70.5 + - - +
146C ALA* 3.7 6.3 - - - +
147C VAL* 3.6 13.9 - - - +
110D PHE* 3.3 36.9 - - + -
124D VAL* 3.8 1.0 - - - +
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Residues in contact with ASN 92 (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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143B ARG* 4.9 3.7 + - - +
90C GLN* 3.7 22.4 - - - +
91C GLN* 1.3 76.4 + - - +
93C VAL* 1.3 76.2 + - - +
94C ASP* 3.4 13.9 + - - +
107C VAL* 3.5 2.5 - - - +
108C CYS* 2.8 52.3 + - - -
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Residues in contact with VAL 93 (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 GLN 4.3 0.4 + - - -
92C ASN* 1.3 79.5 + - - +
94C ASP* 1.3 64.8 + - - +
95C PHE* 3.9 9.9 - - - +
96C VAL* 3.8 28.9 - - + -
106C GLY 3.9 6.1 - - - +
107C VAL* 3.8 18.6 - - + -
139C LEU* 4.4 7.4 - - + -
143C ARG* 3.6 38.7 - - - +
94D ASP* 5.8 0.2 - - - -
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Residues in contact with ASP 94 (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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93B VAL* 5.4 1.0 - - - +
139B LEU* 3.4 15.4 - - + +
143B ARG* 2.6 34.8 + - - -
92C ASN* 3.4 17.7 + - - +
93C VAL* 1.3 73.6 - - - +
95C PHE* 1.3 72.2 + - + +
106C GLY 2.7 15.7 + - - +
126C TYR* 2.5 33.0 + - - +
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Residues in contact with PHE 95 (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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135B LYS* 3.6 38.8 - - + +
136B ALA* 3.4 40.6 - - + -
139B LEU* 3.9 13.2 - - + -
93C VAL* 3.5 3.7 - - - +
94C ASP* 1.3 90.7 - - + +
96C VAL* 1.3 69.2 + - - +
97C ASP* 3.5 19.1 - - - +
104C TYR* 3.2 35.0 - - + -
105C VAL* 3.4 5.2 - - - +
106C GLY* 3.3 37.2 + - - +
126C TYR* 4.1 0.4 - - - -
130C GLU* 5.7 0.2 - - - -
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Residues in contact with VAL 96 (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 VAL* 3.8 18.8 - - + -
95C PHE* 1.3 80.6 - - - +
97C ASP* 1.3 62.7 + - - +
98C LEU 4.3 0.7 + - - -
103C PHE* 4.2 22.2 - - + -
104C TYR 3.6 3.4 - - - -
105C VAL* 4.2 11.2 - - + -
135C LYS* 4.4 23.1 - - + -
139C LEU* 4.1 22.7 - - + -
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Residues in contact with ASP 97 (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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103B PHE* 5.9 0.2 - - - -
135B LYS* 2.8 40.7 + - - +
95C PHE* 3.5 9.1 - - - +
96C VAL* 1.3 81.8 + - - +
98C LEU* 1.3 60.4 + - - +
99C ASN* 3.9 17.4 - - - +
103C PHE* 3.2 8.2 - - - -
104C TYR* 2.6 52.8 + - + +
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Residues in contact with LEU 98 (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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96C VAL 4.3 0.8 + - - -
97C ASP* 1.3 72.6 - - - +
99C ASN* 1.3 67.1 + - - +
100C ASN 3.8 18.8 - - - +
101C GLY* 4.0 12.8 - - - +
102C LYS 3.4 12.8 - - - +
103C PHE* 3.9 32.5 - - + -
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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