Contacts of the strand formed by residues 103 - 115 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96V VAL* 4.2 15.3 - - + -
97V ASP 3.2 13.5 - - - -
98V LEU* 3.8 34.1 - - + -
101V GLY 4.8 0.9 - - - -
102V LYS* 1.3 72.7 - - - +
104V TYR* 1.3 64.7 + - - +
105V VAL* 4.5 3.4 - - + -
129V SER 3.3 7.0 - - - +
130V GLU* 3.6 0.2 - - - -
131V GLY 3.0 22.3 + - - -
132V LEU 2.8 12.5 + - - +
133V LYS* 3.3 31.0 - - - -
134V SER 3.8 0.7 - - - -
135V LYS* 3.5 50.3 - - + -
138V SER* 3.8 19.8 + - - +
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Residues in contact with TYR 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95V PHE* 3.2 18.0 - - + -
96V VAL* 3.5 0.2 - - - -
97V ASP* 2.7 52.3 + - + +
99V ASN* 3.9 24.9 - - + +
100V ASN* 3.4 24.9 + - - -
102V LYS* 3.5 29.7 - - + +
103V PHE* 1.3 72.4 - - - +
105V VAL* 1.3 60.6 + - - +
129V SER 3.4 2.5 - - - -
130V GLU* 3.6 33.4 - - + +
131V GLY* 3.7 17.1 - - - -
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Residues in contact with VAL 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136U ALA* 4.8 0.2 - - - -
93V VAL* 4.7 0.2 - - + -
95V PHE* 3.4 14.3 - - - +
96V VAL* 4.1 21.1 - - + -
103V PHE* 4.5 1.6 - - + -
104V TYR* 1.3 83.3 - - - +
106V GLY* 1.3 62.4 + - - +
107V VAL* 4.0 6.7 - - + -
127V GLY 3.6 0.5 - - - +
128V VAL* 3.4 10.6 - - - +
129V SER* 2.8 38.8 + - - +
130V GLU* 4.9 1.4 - - - +
135V LYS* 6.3 0.2 - - - -
138V SER* 3.8 27.1 - - - +
139V LEU* 3.6 26.9 - - + +
142V ALA* 4.0 17.4 - - + +
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Residues in contact with GLY 106 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136U ALA* 4.5 1.1 - - - -
93V VAL* 3.9 0.2 - - - -
94V ASP* 2.8 29.1 + - - +
95V PHE* 3.2 22.7 + - - +
105V VAL* 1.3 76.5 - - - +
107V VAL* 1.3 64.0 + - - +
126V TYR* 3.3 24.2 - - - -
127V GLY 3.5 4.0 - - - -
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Residues in contact with VAL 107 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91V GLN* 3.7 28.0 - - + +
92V ASN 3.6 11.7 - - - +
93V VAL* 3.8 22.7 - - + -
105V VAL* 4.0 9.2 - - + -
106V GLY* 1.3 80.0 - - - +
108V CYS* 1.3 71.5 + - - +
126V TYR* 3.2 8.6 - - - -
127V GLY 2.6 40.8 + - - -
139V LEU* 4.6 0.9 - - + -
142V ALA* 3.8 27.6 - - + +
143V ARG* 4.1 11.7 - - + +
146V ALA* 3.5 4.7 - - + +
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Residues in contact with CYS 108 (chain V).
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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143U ARG* 3.4 39.0 - - - +
91V GLN* 3.3 6.2 - - - +
92V ASN* 2.8 49.5 + - - -
94V ASP* 4.7 0.2 + - - -
107V VAL* 1.3 75.2 - - - +
109V ALA* 1.3 60.5 + - - +
110V PHE* 3.8 18.6 - - - -
124V VAL* 4.5 4.9 - - + -
125V GLY 3.3 8.1 - - - +
126V TYR* 3.6 21.7 - - + -
146V ALA* 4.1 2.0 - - - -
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Residues in contact with ALA 109 (chain V).
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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88V ILE* 5.1 2.0 - - + -
90V GLN 3.4 9.4 - - - +
91V GLN* 4.0 11.2 - - + +
108V CYS* 1.3 75.4 - - - +
110V PHE* 1.3 65.6 + - - +
111V VAL* 3.9 7.7 + - + +
123V ASP 3.6 0.9 - - - +
124V VAL* 3.2 3.9 - - - -
125V GLY* 2.8 31.8 + - - -
146V ALA* 3.7 30.0 - - + +
147V VAL* 3.9 13.0 - - + +
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Residues in contact with PHE 110 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88U ILE* 3.7 29.6 - - + -
91U GLN* 3.2 44.9 - - + -
143U ARG* 4.5 4.7 - - - -
88V ILE* 3.5 4.9 - - - -
89V THR* 2.8 45.1 + - - +
90V GLN* 2.7 41.3 + - + +
92V ASN* 5.6 0.2 - - + -
108V CYS* 3.8 23.6 - - - -
109V ALA* 1.3 71.9 - - - +
111V VAL* 1.3 62.6 + - - +
122V GLU* 3.8 6.1 - - - +
123V ASP 3.4 2.7 - - - +
124V VAL* 3.0 24.5 - - + -
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Residues in contact with VAL 111 (chain V).
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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86V HIS* 3.9 26.2 - - + -
87V SER 3.4 11.0 - - - +
88V ILE* 4.7 4.7 - - + -
109V ALA* 4.5 7.0 - - + -
110V PHE* 1.3 78.5 - - - +
112V ARG* 1.3 63.0 + - - +
122V GLU* 3.3 4.0 - - - -
123V ASP 3.0 29.9 + - - +
147V VAL* 3.7 35.9 - - + +
150V GLY* 3.8 15.7 - - - +
151V LEU* 3.8 22.9 - - + +
154V ALA* 3.7 7.3 - - + +
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Residues in contact with ARG 112 (chain V).
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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120L TYR* 5.0 5.4 + - - -
87U SER* 5.1 4.8 - - - -
86V HIS* 3.1 3.9 - - - -
87V SER* 2.9 42.9 + - - +
89V THR* 3.9 23.3 - - + +
110V PHE 4.1 1.0 + - - -
111V VAL* 1.3 71.9 - - - +
113V VAL* 1.3 63.6 + - - +
114V GLN* 3.1 33.2 + - - +
118V GLY 4.8 0.8 + - - -
120V TYR* 3.4 47.9 - - + +
121V HIS 3.6 6.3 - - - +
122V GLU* 3.8 25.4 - - + -
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Residues in contact with VAL 113 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84V TRP* 4.1 11.2 - - + -
85V ALA 3.1 12.8 - - - +
86V HIS* 4.0 7.4 - - + +
111V VAL 4.1 0.2 + - - -
112V ARG* 1.3 75.8 - - - +
114V GLN* 1.3 67.5 + - - +
120V TYR* 3.2 6.5 - - - +
121V HIS 2.9 42.2 + - - +
151V LEU* 4.8 3.6 - - + -
154V ALA* 3.4 30.7 - - + -
155V LEU* 3.6 24.2 - - + +
158V PHE* 4.0 19.4 - - + -
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Residues in contact with GLN 114 (chain V).
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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120L TYR* 3.2 22.1 + - - +
26V PHE* 3.4 14.8 - - + -
27V GLY* 3.5 24.5 - - - -
84V TRP* 3.1 4.5 - - - +
85V ALA 2.7 40.5 + - - +
112V ARG* 3.1 26.0 + - - +
113V VAL* 1.3 76.5 - - - +
115V LEU* 1.3 81.1 + - - +
118V GLY* 3.5 15.1 - - - +
119V SER 3.2 13.5 - - - +
120V TYR* 4.2 4.0 - - + +
158V PHE* 5.3 0.2 - - - -
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Residues in contact with LEU 115 (chain V).
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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81U TYR* 4.1 13.9 - - + -
26V PHE* 3.4 3.8 - - - -
31V TYR* 3.6 18.4 - - + +
79V PHE* 4.0 20.9 - - + -
83V GLY 3.3 4.3 - - - +
84V TRP* 3.8 19.1 - - + -
113V VAL* 5.0 0.4 - - + -
114V GLN* 1.3 92.4 + - - +
116V LYS* 1.3 58.4 + - - +
117V ASP* 2.8 14.3 + - + -
118V GLY 2.9 12.3 + - - -
119V SER* 2.9 28.3 + - - +
158V PHE* 3.2 48.0 - - + -
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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