Contacts of the strand formed by residues 136 - 147 (chain A) in PDB entry 4H3I
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 LYS 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A TYR* 3.5 33.2 + - + +
130A VAL* 3.0 19.7 - - - +
131A PRO* 3.5 8.3 - - + -
135A GLY* 1.3 77.3 - - - +
137A TRP* 1.3 63.0 + - - +
138A GLU* 6.3 1.3 - - + -
166A SER* 3.4 2.3 - - - -
167A ASP* 2.7 66.8 + - + +
169A PHE* 4.1 7.3 - - - +
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Residues in contact with TRP 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ASN* 4.7 9.0 - - + -
100A ALA* 3.6 26.4 - - + +
128A VAL* 3.7 29.4 - - + -
129A TYR* 3.9 1.0 - - - -
130A VAL* 2.9 67.2 + - + +
136A LYS* 1.3 76.9 - - - +
138A GLU* 1.3 73.8 + - - +
139A GLY 4.3 1.3 - - - -
161A ALA* 3.8 15.5 - - + -
163A ILE* 3.8 28.3 - - + -
165A GLU 3.3 12.3 - - - +
166A SER* 4.0 5.8 - - - +
169A PHE* 3.5 42.0 - + + -
179A ILE* 5.0 3.5 - - + +
502A 10V 4.1 18.6 + + - -
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Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A VAL 3.4 7.4 - - - +
129A TYR* 3.3 38.4 - - + +
136A LYS* 6.2 1.6 - - + -
137A TRP* 1.3 79.2 - - - +
139A GLY* 1.3 59.0 + - - +
163A ILE* 3.5 3.8 - - - -
164A THR* 3.1 22.6 + - - +
165A GLU* 2.7 40.5 + - + +
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Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLY* 3.5 4.3 - - - -
128A VAL* 2.9 40.7 + - - +
137A TRP* 4.1 2.4 - - - -
138A GLU* 1.3 77.5 - - - +
140A GLU* 1.3 66.0 + - - +
162A ALA 3.0 16.6 - - - -
163A ILE* 4.1 0.7 - - - -
164A THR* 4.1 5.6 - - - -
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ARG* 2.6 41.3 + - - +
121A TYR* 5.6 1.2 + - - +
123A ASP* 5.6 2.7 - - - +
126A LYS 3.8 5.8 - - - +
127A GLY* 5.5 2.0 - - - -
139A GLY* 1.3 77.9 - - - +
141A LEU* 1.3 67.3 + - - +
160A ILE 3.6 0.9 - - - +
161A ALA* 4.5 0.9 - - - -
162A ALA* 2.9 32.6 + - - +
164A THR* 4.1 21.6 + - + +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 4.6 2.6 + - - -
123A ASP* 3.5 9.0 - - - +
124A LEU* 3.1 34.7 + - + +
125A ARG 4.0 1.4 + - - -
126A LYS* 2.8 52.4 + - + +
127A GLY 4.1 1.3 - - - +
128A VAL* 3.9 23.6 - - + -
140A GLU* 1.3 74.7 - - - +
142A GLY* 1.3 59.4 + - - +
160A ILE 3.6 4.3 - - - +
161A ALA* 4.0 16.4 - - + +
190A PRO* 3.8 21.1 - - + -
194A LEU* 3.8 34.3 - - + -
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TYR* 4.4 10.1 - - - -
122A ARG 3.0 15.0 - - - -
124A LEU* 3.7 10.7 - - - +
140A GLU 3.8 0.2 + - - -
141A LEU* 1.3 76.5 - - - +
143A THR* 1.3 63.2 + - - +
159A ASN* 3.4 2.4 - - - -
160A ILE* 2.7 38.1 + - - -
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Residues in contact with THR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 5.0 0.2 - - - -
121A TYR* 3.6 4.2 - - - -
122A ARG* 2.8 46.4 + - + +
124A LEU* 3.9 17.3 - - + -
142A GLY* 1.3 78.7 - - - +
144A ASP* 1.3 64.8 + - - +
157A ARG* 3.0 29.0 + - + -
158A ALA 3.2 12.8 - - - +
159A ASN* 3.5 20.9 - - - +
160A ILE* 4.5 2.5 - - - +
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Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLY* 3.3 15.0 - - - +
113A TYR* 2.5 27.7 + - - +
118A SER* 2.7 22.5 + - - -
120A THR* 2.7 28.6 + - - -
121A TYR* 3.4 12.3 - - - -
143A THR* 1.3 75.7 + - - +
145A LEU* 1.3 66.9 + - - +
146A VAL* 3.6 3.6 + - - +
157A ARG* 3.3 13.0 - - - +
158A ALA 3.0 28.7 + - - +
160A ILE* 3.7 13.6 - - + +
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A THR 4.0 0.2 - - - +
81A VAL* 3.5 3.6 - - - -
82A GLY 3.0 28.3 + - - +
83A SER* 3.9 11.2 - - - +
120A THR* 3.8 32.8 - - + +
144A ASP* 1.3 81.1 + - - +
146A VAL* 1.3 60.2 + - - +
155A THR* 3.8 21.1 - - + -
156A VAL 3.4 3.6 - - - +
157A ARG* 3.9 38.6 - - + +
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A MET* 3.6 31.0 - - + -
80A THR 3.3 11.2 - - - +
81A VAL* 4.0 5.2 - - + -
99A PHE* 3.8 26.2 - - + -
144A ASP 3.7 11.2 - - - +
145A LEU* 1.3 80.5 - - - +
147A SER* 1.3 71.1 + - - +
155A THR* 3.5 1.2 - - - +
156A VAL* 2.7 40.7 + - - +
158A ALA* 4.4 9.0 - - + -
160A ILE* 4.0 13.0 - - + -
197A PHE* 4.0 14.3 - - + -
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Residues in contact with SER 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A MET* 3.4 8.1 - - - +
80A THR* 3.0 42.9 + - - -
146A VAL* 1.3 76.2 + - - +
148A ILE* 1.3 66.5 + - - +
149A PRO* 3.9 4.0 - - - -
154A VAL 3.9 10.5 - - - -
155A THR* 2.9 29.1 + - - +
197A PHE* 6.1 0.9 - - - -
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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