Contacts of the strand formed by residues 120 - 130 (chain Q) 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 TYR 120 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26P PHE* 3.9 12.1 - + - -
84P TRP 4.9 0.4 + - - -
85P ALA* 2.9 48.9 - - + +
86P HIS* 3.6 26.1 - - - -
87P SER* 4.0 13.1 + - - -
112P ARG* 5.1 4.2 + - - -
114P GLN* 3.3 30.2 + - - +
112Q ARG* 3.6 46.2 - - + +
113Q VAL 3.2 16.8 - - - +
114Q GLN* 4.2 0.9 - - - +
118Q GLY 3.1 18.2 - - - -
119Q SER* 1.3 77.3 - - - +
121Q HIS* 1.3 69.6 + - - +
158Q PHE* 4.8 3.5 - - - -
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Residues in contact with HIS 121 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P TYR 4.4 3.8 - - - -
84P TRP* 3.3 44.3 + + - -
86P HIS* 2.7 43.1 - + + -
112Q ARG* 4.5 2.0 - - - -
113Q VAL* 2.9 38.4 + - + +
119Q SER* 6.2 0.2 - - - -
120Q TYR* 1.3 85.8 + - - +
122Q GLU* 1.3 61.3 + - - +
154Q ALA* 3.7 8.9 - - - +
157Q SER* 3.3 37.4 - - - +
158Q PHE* 3.7 33.4 - + - -
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Residues in contact with GLU 122 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86P HIS* 3.0 37.4 + - - +
87P SER* 3.5 12.6 - - - -
88P ILE* 2.9 47.9 + - + +
147P VAL* 4.7 0.5 - - - +
89Q THR* 2.6 39.0 + - - +
110Q PHE* 3.8 6.8 - - - +
111Q VAL 3.2 18.6 - - - +
112Q ARG* 3.9 12.9 - - + +
121Q HIS* 1.3 78.2 - - - +
123Q ASP* 1.3 67.0 + - - +
154Q ALA* 4.5 1.1 - - - -
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Residues in contact with ASP 123 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86P HIS* 5.0 4.7 + - + +
88P ILE* 3.7 11.0 - - - -
147P VAL* 3.5 18.0 - - - +
148P THR* 5.1 3.1 + - - -
151P LEU* 6.2 0.3 - - - +
110Q PHE* 3.4 4.9 - - - +
111Q VAL* 3.0 33.2 + - - +
122Q GLU* 1.3 76.2 - - - +
124Q VAL* 1.3 71.8 + - - +
150Q GLY 4.5 1.8 - - - +
153Q ARG* 2.4 53.0 + - + +
154Q ALA* 3.8 23.9 - - + +
157Q SER* 5.2 2.6 + - - -
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Residues in contact with VAL 124 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P GLN* 3.8 6.7 - - - +
143P ARG* 3.8 21.3 - - + +
144P LYS* 4.2 4.6 - - + -
147P VAL* 3.1 32.5 - - + -
108Q CYS* 4.5 6.7 - - + -
109Q ALA 3.3 7.9 - - - +
110Q PHE* 3.1 38.8 - - + -
123Q ASP* 1.3 88.7 + - - +
125Q GLY* 1.3 66.1 + - - +
126Q TYR* 6.2 0.7 - - + -
150Q GLY* 4.0 2.7 - - - -
153Q ARG* 2.9 32.7 + - - +
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Residues in contact with GLY 125 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144P LYS* 4.5 1.3 - - - -
108Q CYS* 3.3 7.1 - - - +
109Q ALA 2.7 29.6 + - - -
124Q VAL* 1.3 77.3 - - - +
126Q TYR* 1.3 61.2 + - - +
146Q ALA* 3.5 9.0 - - - -
149Q ASP* 3.4 11.2 - - - -
150Q GLY* 3.4 22.3 - - - -
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Residues in contact with TYR 126 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136P ALA 3.6 14.6 - - - -
139P LEU* 3.5 16.0 - - + +
140P GLU* 3.5 46.0 - - + +
143P ARG* 3.7 17.7 - - + -
144P LYS* 4.0 4.7 - - + +
94Q ASP* 2.7 33.1 + - - +
95Q PHE* 4.0 2.4 - - - -
106Q GLY* 3.2 31.3 - - - -
107Q VAL 3.2 19.1 - - - -
108Q CYS* 3.7 10.1 - - + -
124Q VAL* 6.2 0.2 - - + -
125Q GLY* 1.3 73.4 - - - -
127Q GLY* 1.3 67.4 + - - +
128Q VAL* 3.7 15.8 + - + +
145Q GLU* 3.9 2.9 - - - +
146Q ALA* 3.6 8.6 - - - -
149Q ASP* 2.9 20.4 + - - +
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Residues in contact with GLY 127 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Q GLY* 3.6 3.5 - - - -
107Q VAL 2.6 37.5 + - - -
126Q TYR* 1.3 74.6 - - - +
128Q VAL* 1.3 63.3 + - - +
142Q ALA* 3.3 32.3 - - - +
145Q GLU* 4.1 5.6 - - - -
146Q ALA* 3.5 6.5 - - - +
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Residues in contact with VAL 128 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136P ALA* 3.6 32.3 - - + +
137P LEU* 4.6 8.3 - - + -
140P GLU* 4.8 12.6 - - - +
105Q VAL 3.5 2.9 - - - +
126Q TYR* 3.7 19.5 + - + -
127Q GLY* 1.3 79.4 - - - +
129Q SER* 1.3 61.1 + - - +
130Q GLU* 3.8 23.3 - - + +
141Q LYS* 2.6 35.0 + - - +
142Q ALA* 4.1 2.9 - - - +
145Q GLU* 3.6 7.1 + - - +
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Residues in contact with SER 129 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q PHE 3.4 5.4 - - - +
104Q TYR* 3.5 0.2 - - - -
105Q VAL* 2.8 38.5 + - - +
128Q VAL* 1.3 77.6 - - - +
130Q GLU* 1.3 61.5 + - - +
132Q LEU* 3.7 14.7 - - - +
138Q SER* 3.2 49.4 + - - -
141Q LYS* 4.0 14.4 - - - +
142Q ALA* 4.4 1.1 - - - +
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Residues in contact with GLU 130 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134P SER* 2.7 31.1 + - - -
135P LYS 4.8 0.5 + - - -
136P ALA* 3.9 8.3 + - + +
137P LEU* 3.8 10.9 - - - +
95Q PHE* 5.8 0.3 - - - -
103Q PHE 3.5 2.7 - - - -
104Q TYR* 3.6 31.7 - - + +
105Q VAL 4.8 0.4 - - - +
128Q VAL* 3.8 19.6 - - + +
129Q SER* 1.3 81.8 + - - +
131Q GLY* 1.3 59.8 + - - +
132Q LEU* 3.7 5.0 + - - +
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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