Contacts of the strand formed by residues 103 - 115 (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 PHE 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C VAL* 4.2 15.5 - - + -
97C ASP 3.2 12.8 - - - -
98C LEU* 3.9 32.1 - - + -
101C GLY 4.8 1.3 - - - -
102C LYS* 1.3 71.9 - - - +
104C TYR* 1.3 63.4 + - - +
105C VAL* 4.1 4.9 - - + -
129C SER 3.4 6.0 - - - +
131C GLY* 2.9 27.5 + - - -
132C LEU 2.8 11.2 + - - -
133C LYS* 3.2 32.3 - - - -
134C SER 3.8 0.7 - - - -
135C LYS* 3.5 52.0 - - + -
138C SER* 3.7 20.8 + - - +
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Residues in contact with TYR 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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95C PHE* 3.2 17.4 - - + -
97C ASP* 2.6 48.9 + - + +
99C ASN* 3.9 24.9 - - + +
100C ASN* 3.4 23.4 + - - -
102C LYS* 3.4 34.6 - - + +
103C PHE* 1.3 72.5 - - - +
105C VAL* 1.3 60.5 + - - +
129C SER 3.4 2.7 - - - -
130C GLU* 3.6 31.6 - - + +
131C GLY* 3.8 17.1 - - - -
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Residues in contact with VAL 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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136B ALA* 4.4 0.2 - - - +
93C VAL* 4.8 0.2 - - + -
95C PHE* 3.4 15.0 - - - +
96C VAL* 4.2 19.3 - - + -
103C PHE* 4.4 2.0 - - + -
104C TYR* 1.3 84.2 - - - +
106C GLY* 1.3 62.1 + - - +
107C VAL* 4.1 6.7 - - + -
127C GLY 3.6 0.5 - - - +
128C VAL* 3.4 10.9 - - - +
129C SER* 2.7 42.1 + - - +
130C GLU* 4.9 1.0 - - - +
135C LYS* 6.3 0.4 - - + -
138C SER* 3.8 27.1 - - - +
139C LEU* 3.7 28.0 - - + +
142C ALA* 3.9 13.7 - - + -
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Residues in contact with GLY 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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136B ALA* 4.5 0.9 - - - -
93C VAL 3.7 0.2 - - - -
94C ASP* 2.7 34.5 + - - +
95C PHE* 3.3 22.0 + - - +
105C VAL* 1.3 75.9 - - - +
107C VAL* 1.3 60.3 + - - +
126C TYR* 3.3 24.2 - - - -
127C GLY 3.5 4.3 - - - -
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Residues in contact with VAL 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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91C GLN* 3.6 36.1 - - + +
92C ASN 3.5 11.7 - - - +
93C VAL* 3.8 22.2 - - + -
105C VAL* 4.1 9.4 - - + -
106C GLY* 1.3 80.2 - - - +
108C CYS* 1.3 64.2 + - - +
126C TYR* 3.2 9.5 - - - -
127C GLY 2.7 37.2 + - - -
139C LEU* 4.7 0.4 - - + -
142C ALA* 3.7 31.2 - - + +
143C ARG* 4.1 7.9 - - + +
146C ALA* 3.6 4.1 - - + +
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Residues in contact with CYS 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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143B ARG* 3.3 38.8 - - - -
91C GLN* 3.3 5.5 - - - +
92C ASN* 2.8 54.1 + - - -
94C ASP* 4.7 0.2 + - - -
107C VAL* 1.3 74.4 - - - +
109C ALA* 1.3 59.3 + - - +
110C PHE* 3.7 20.2 - - - -
124C VAL* 4.5 4.7 - - + -
125C GLY 3.3 6.7 - - - +
126C TYR* 3.6 20.6 - - + -
146C ALA* 4.1 1.8 - - - -
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Residues in contact with ALA 109 (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* 5.0 2.5 - - + -
90C GLN 3.4 7.4 - - - +
91C GLN* 3.9 11.4 - - + +
108C CYS* 1.3 76.2 - - - +
110C PHE* 1.3 64.6 + - - +
111C VAL* 3.9 6.8 + - + +
123C ASP 3.7 0.5 - - - +
124C VAL* 3.2 5.4 - - - +
125C GLY 2.7 35.4 + - - -
146C ALA* 3.6 30.7 - - + +
147C VAL* 3.8 13.7 - - + +
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Residues in contact with PHE 110 (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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88B ILE* 3.8 32.8 - - + -
91B GLN* 3.2 44.2 - - + -
143B ARG* 4.5 3.8 - - - -
88C ILE* 3.5 5.5 - - - -
89C THR* 2.8 44.4 + - - +
90C GLN* 2.8 41.5 + - + +
108C CYS* 3.7 23.8 - - - -
109C ALA* 1.3 72.5 - - - +
111C VAL* 1.3 59.5 + - - +
122C GLU* 3.8 5.6 - - - +
123C ASP 3.4 3.1 - - - +
124C VAL* 3.1 25.6 - - + -
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Residues in contact with VAL 111 (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* 4.1 25.6 - - + -
87C SER 3.3 12.1 - - - +
88C ILE* 4.6 9.0 - - + -
109C ALA* 4.4 7.6 - - + -
110C PHE* 1.3 78.5 - - - +
112C ARG* 1.3 61.3 + - - +
113C VAL 4.9 0.2 - - - +
122C GLU* 3.2 5.3 - - - +
123C ASP 3.1 30.8 + - - -
147C VAL* 3.7 31.0 - - + +
150C GLY* 3.8 15.7 - - - +
151C LEU* 3.8 23.1 - - + +
154C ALA* 3.7 7.1 - - + +
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Residues in contact with ARG 112 (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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87B SER* 5.2 3.9 - - - -
86C HIS* 3.1 4.2 - - - -
87C SER* 2.9 44.2 + - - +
89C THR* 4.1 17.7 - - + +
110C PHE 4.2 0.6 + - - -
111C VAL* 1.3 72.7 - - - +
113C VAL* 1.3 64.2 + - - +
114C GLN* 2.9 34.1 + - - +
118C GLY 4.7 0.8 + - - -
120C TYR* 3.4 48.4 - - + +
121C HIS 3.5 6.5 - - - +
122C GLU* 4.0 24.2 - - + -
120D TYR* 5.1 5.2 + - - -
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Residues in contact with VAL 113 (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* 4.2 10.5 - - + -
85C ALA 3.1 13.2 - - - +
86C HIS* 4.0 7.2 - - + +
111C VAL* 4.1 0.4 - - + -
112C ARG* 1.3 75.4 - - - +
114C GLN* 1.3 68.5 + - - +
120C TYR* 3.1 21.7 - - - +
121C HIS 2.8 26.6 + - - +
151C LEU* 4.8 3.4 - - + -
154C ALA* 3.4 31.6 - - + +
155C LEU* 3.5 26.5 - - + +
158C PHE* 3.9 19.1 - - + -
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Residues in contact with GLN 114 (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* 3.4 17.0 - - + -
27C GLY* 3.5 17.8 - - - -
84C TRP* 3.1 3.3 - - - +
85C ALA 2.7 40.8 + - - +
112C ARG* 2.9 25.6 + - - +
113C VAL* 1.3 77.3 - - - +
115C LEU* 1.3 81.5 + - - +
118C GLY* 3.5 20.4 - - - +
119C SER 3.2 14.1 - - - +
120C TYR* 4.2 3.4 - - + -
158C PHE* 5.3 0.2 - - - -
120D TYR* 3.5 21.0 + - - +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B TYR* 4.0 23.3 - - + -
26C PHE* 3.5 4.4 - - - -
31C TYR* 3.6 15.5 - - + +
79C PHE* 4.0 15.9 - - + -
83C GLY 3.3 10.3 - - - +
84C TRP* 3.9 12.8 - - + -
113C VAL* 4.9 0.2 - - + -
114C GLN* 1.3 89.9 + - - +
116C LYS* 1.3 56.0 + - - +
117C ASP* 2.8 8.3 - - + -
118C GLY 2.8 21.0 + - - -
119C SER* 2.8 28.7 + - - +
158C PHE* 3.2 48.2 - - + -
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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