Contacts of the strand formed by residues 154 - 159 (chain A) in PDB entry 2HGM
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 GLU 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ARG* 2.7 41.4 + - - +
115A LEU 3.0 18.2 - - - +
116A ARG* 3.6 20.1 - - + +
118A LEU* 3.8 5.7 - - - +
143A LEU* 4.6 1.2 - - - +
144A PRO* 3.6 17.5 - - + +
145A VAL* 3.0 34.6 + - - +
146A ASP 4.1 11.0 - - - +
147A PRO* 4.3 8.1 - - - +
152A THR* 4.3 2.6 - - - -
153A GLY* 1.3 78.2 + - - +
155A ALA* 1.3 62.5 + - - +
156A PHE* 5.2 3.6 - - + -
193A SER* 5.1 5.4 + - - -
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Residues in contact with ALA 155 (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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114A ARG* 3.3 0.9 - - - +
115A LEU* 2.7 38.0 + - + +
118A LEU* 3.6 13.0 - - + -
127A ILE* 3.5 26.5 - - + -
142A THR 3.2 15.5 - - - +
143A LEU* 3.9 7.0 - - + -
144A PRO* 4.1 0.7 - - - -
154A GLU* 1.3 76.6 - - - +
156A PHE* 1.3 73.4 + - - +
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Residues in contact with PHE 156 (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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112A PHE* 4.5 1.6 - - + -
113A VAL 2.9 10.3 - - - +
114A ARG* 3.2 56.8 - - + -
115A LEU* 4.1 2.2 - - - +
127A ILE* 4.5 1.0 - - - +
141A ILE* 3.3 7.1 - - - +
142A THR* 2.8 41.3 + - + +
144A PRO* 3.9 19.5 - - + -
154A GLU* 5.1 3.1 - - - -
155A ALA* 1.3 93.9 - - - +
157A VAL* 1.3 64.4 + - - +
186A SER* 3.8 5.2 - - - -
190A GLU* 3.4 20.6 - - - -
191A VAL* 3.3 55.6 - - + -
193A SER* 4.6 5.6 - - - -
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Residues in contact with VAL 157 (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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112A PHE* 3.1 8.0 - - - -
113A VAL* 2.8 42.2 + - + -
115A LEU* 4.0 4.7 - - + -
127A ILE* 3.9 7.4 - - + -
131A PHE* 3.6 31.9 - - + -
136A ILE* 3.5 31.0 - - + -
140A GLY 3.2 17.0 - - - +
141A ILE* 3.8 10.1 - - + +
156A PHE* 1.3 77.8 - - - +
158A GLN* 1.3 56.2 + - - +
159A PHE* 3.3 24.5 - - + -
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Residues in contact with GLN 158 (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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109A ASN 2.7 27.3 + - - -
110A ASP* 2.9 17.3 - - - -
111A GLY* 3.1 13.4 + - - -
112A PHE* 2.8 53.4 - - + -
136A ILE* 3.1 23.2 - - - +
137A VAL* 3.5 19.1 + - + +
140A GLY* 2.7 18.1 + - - +
157A VAL* 1.3 69.5 - - - +
159A PHE* 1.3 84.3 + - - +
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Residues in contact with PHE 159 (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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111A GLY 2.9 8.7 + - - +
113A VAL* 3.3 21.3 - - + -
131A PHE* 3.6 22.9 - + + -
134A LEU* 3.6 22.4 - - + -
135A GLU 3.3 19.7 - - - +
136A ILE* 3.7 9.9 - - + +
137A VAL* 3.5 9.1 - - - +
157A VAL* 3.3 27.1 - - + -
158A GLN* 1.3 94.1 + - - +
160A ALA* 1.3 61.2 + - - +
161A SER 3.3 17.9 - - - +
164A LEU* 3.4 29.4 - - + -
165A ALA* 3.6 14.1 - - + -
168A ALA* 3.1 22.4 - - + -
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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