Contacts of the strand formed by residues 103 - 115 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96M VAL* 4.2 12.8 - - + -
97M ASP 3.2 15.3 - - - -
98M LEU* 3.8 35.4 - - + -
101M GLY 4.8 1.8 - - - -
102M LYS* 1.3 73.1 - - - +
104M TYR* 1.3 64.0 + - - +
105M VAL* 4.1 4.3 - - + -
129M SER 3.5 5.5 - - - +
130M GLU 3.6 0.2 - - - -
131M GLY* 2.9 25.1 + - - -
132M LEU 2.8 10.2 + - - -
133M LYS* 3.3 28.7 - - - -
134M SER 3.8 0.4 - - - -
135M LYS* 3.5 52.9 - - + -
138M SER* 3.8 20.6 + - - +
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Residues in contact with TYR 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95M PHE* 3.4 17.3 - - + -
97M ASP* 2.6 51.6 + - + +
99M ASN* 3.9 25.6 - - + +
100M ASN* 3.4 25.1 + - - -
102M LYS* 3.4 33.8 + - + +
103M PHE* 1.3 71.3 - - - +
105M VAL* 1.3 61.7 + - - +
129M SER 3.5 2.2 - - - -
130M GLU* 3.6 40.6 - - + +
131M GLY* 3.8 9.8 - - - -
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Residues in contact with VAL 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95M PHE* 3.4 15.2 - - - +
96M VAL* 4.1 20.4 - - + -
103M PHE* 4.5 2.2 - - + -
104M TYR* 1.3 85.5 - - - +
106M GLY* 1.3 60.8 + - - +
107M VAL* 4.0 6.7 - - + -
127M GLY 3.7 0.3 - - - +
128M VAL* 3.4 10.4 - - - +
129M SER 2.8 36.1 + - - +
130M GLU* 4.9 1.0 - - - +
135M LYS* 5.4 0.4 - - - +
138M SER* 3.8 28.5 - - - +
139M LEU* 3.6 27.8 - - + +
142M ALA* 3.8 19.9 - - + +
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Residues in contact with GLY 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136L ALA* 4.6 0.9 - - - -
93M VAL* 3.9 0.2 - - - -
94M ASP* 2.7 28.1 + - - +
95M PHE* 3.3 23.0 + - - +
105M VAL* 1.3 75.0 - - - +
107M VAL* 1.3 64.3 + - - +
126M TYR* 3.5 23.8 - - - -
127M GLY 3.6 4.5 - - - -
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Residues in contact with VAL 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M GLN* 3.7 36.3 - - + +
92M ASN 3.6 11.2 - - - +
93M VAL* 3.9 22.4 - - + +
94M ASP 4.3 0.2 - - - +
105M VAL* 4.0 9.0 - - + -
106M GLY* 1.3 80.0 - - - +
108M CYS* 1.3 66.0 + - - +
126M TYR* 3.2 9.7 - - - -
127M GLY 2.7 35.1 + - - -
139M LEU* 4.7 0.2 - - + -
142M ALA* 3.8 28.9 - - + +
143M ARG* 4.0 10.1 - - + -
146M ALA* 3.5 4.7 - - + +
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Residues in contact with CYS 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143L ARG* 3.4 36.8 - - - -
91M GLN* 3.3 4.9 - - - +
92M ASN* 2.9 52.6 + - - -
107M VAL* 1.3 75.2 - - - +
109M ALA* 1.3 61.2 + - - +
110M PHE* 3.7 18.4 - - - -
124M VAL* 4.4 5.8 - - + -
125M GLY 3.3 8.1 - - - +
126M TYR* 3.7 20.2 - - + -
146M ALA* 4.0 2.9 - - - -
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Residues in contact with ALA 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M ILE* 5.0 2.0 - - + -
90M GLN 3.4 6.7 - - - +
91M GLN* 3.9 11.7 - - + +
108M CYS* 1.3 75.4 - - - +
110M PHE* 1.3 65.1 + - - +
111M VAL* 3.9 7.7 + - + +
123M ASP 3.7 0.3 - - - +
124M VAL* 3.2 4.7 - - - +
125M GLY 2.8 31.1 + - - -
146M ALA* 3.5 31.1 - - + +
147M VAL* 3.8 13.5 - - + +
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Residues in contact with PHE 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L ILE* 3.7 31.2 - - + -
91L GLN* 3.2 43.7 - - + -
143L ARG* 4.5 4.3 - - - -
88M ILE* 3.4 4.2 - - - -
89M THR* 2.7 49.3 + - - +
90M GLN* 2.7 41.0 + - + +
108M CYS* 3.7 24.9 - - - -
109M ALA* 1.3 73.6 - - - +
111M VAL* 1.3 55.7 + - - +
122M GLU* 3.7 6.1 - - - +
123M ASP 3.5 3.6 - - - +
124M VAL* 3.1 22.4 - - + -
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Residues in contact with VAL 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M HIS* 3.9 26.5 - - + -
87M SER 3.4 11.7 - - - +
88M ILE* 4.6 4.9 - - + -
109M ALA* 4.4 6.5 - - + -
110M PHE* 1.3 78.1 - - - +
112M ARG* 1.3 62.8 + - - +
122M GLU* 3.2 4.5 - - - -
123M ASP 3.0 29.6 + - - -
147M VAL* 3.6 36.3 - - + +
150M GLY* 3.7 16.4 - - - +
151M LEU* 3.7 21.5 - - + +
154M ALA* 3.8 7.0 - - + +
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Residues in contact with ARG 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L SER* 5.2 5.0 - - - -
86M HIS* 3.1 3.5 - - - -
87M SER* 2.9 40.6 + - - +
89M THR* 4.0 23.1 - - + +
110M PHE 4.1 0.8 + - - -
111M VAL* 1.3 71.0 - - - +
113M VAL* 1.3 67.1 + - - +
114M GLN* 2.9 34.6 + - - +
118M GLY 4.8 0.6 + - - -
120M TYR* 3.5 46.4 - - + +
121M HIS 3.5 6.3 - - - +
122M GLU* 3.8 25.6 - - + -
120N TYR* 5.0 5.8 + - - -
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Residues in contact with VAL 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M TRP* 4.0 12.6 - - + -
85M ALA 3.1 13.7 - - - +
86M HIS* 4.1 7.2 - - + -
111M VAL* 5.4 0.2 - - + -
112M ARG* 1.3 76.2 - - - +
114M GLN* 1.3 67.8 + - - +
120M TYR* 3.2 7.4 - - - +
121M HIS 2.8 40.6 + - - +
151M LEU* 4.7 3.8 - - + -
154M ALA* 3.4 33.2 - - + +
155M LEU* 3.4 27.1 - - + -
158M PHE* 4.1 14.7 - - + -
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Residues in contact with GLN 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M PHE* 3.4 16.0 - - + -
27M GLY* 3.6 20.4 - - - -
84M TRP* 3.1 3.6 - - - +
85M ALA 2.8 36.6 + - - +
112M ARG* 2.9 29.9 + - - +
113M VAL* 1.3 76.9 - - - +
115M LEU* 1.3 72.0 + - - +
118M GLY* 3.5 24.2 - - - +
119M SER 3.3 12.8 - - - +
158M PHE* 5.4 0.2 - - - -
120N TYR* 3.2 23.2 + - - +
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Residues in contact with LEU 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L TYR* 3.9 21.1 - - + -
26M PHE* 3.6 3.7 - - - -
31M TYR* 3.5 20.0 - - + +
79M PHE* 4.0 15.0 - - + -
83M GLY 3.2 9.9 - - - +
84M TRP* 3.9 13.2 - - + -
113M VAL* 5.1 0.4 - - + -
114M GLN* 1.3 88.9 + - - +
116M LYS* 1.3 54.2 + - - +
117M ASP* 2.8 17.2 + - + -
118M GLY 2.8 13.9 + - - -
119M SER* 2.9 28.5 + - - +
158M PHE* 3.3 45.3 - - + -
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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