Contacts of the strand formed by residues 157 - 162 (chain A) in PDB entry 1GC5
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 ILE 157 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ALA* 3.9 23.1 - - + +
127A ASN* 3.6 22.7 - - - +
130A GLY* 4.0 10.5 - - - -
131A GLY* 4.1 9.6 - - - +
137A THR* 3.5 6.3 - - - +
139A VAL* 4.0 23.1 - - + -
152A PHE* 4.0 16.8 - - + -
153A VAL 3.2 27.8 - - - +
155A GLY 2.7 12.5 + - - +
156A PRO* 1.3 74.8 - - - +
158A TYR* 1.3 63.0 + - - +
171A HIS* 2.8 24.6 - - - -
172A PRO* 3.5 16.9 - - + +
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Residues in contact with TYR 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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136A PRO* 4.6 10.1 - - + -
137A THR 2.7 20.4 + - - +
138A ILE* 3.3 12.7 - - + -
139A VAL* 3.0 32.0 + - - +
156A PRO* 3.4 35.7 - - + +
157A ILE* 1.3 74.1 - - - +
159A VAL* 1.3 61.1 + - - +
169A LEU* 4.0 37.5 - - + -
170A VAL* 3.5 7.0 - - - +
171A HIS* 3.1 37.2 + + - -
172A PRO* 4.8 1.3 - - - -
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 3.5 21.1 - - + +
141A VAL* 3.7 26.9 - - + +
144A ASN* 5.3 3.1 - - - +
158A TYR* 1.3 74.4 - - - +
160A PRO* 1.3 70.5 - - + +
161A VAL* 3.6 7.8 + - + +
169A LEU* 3.5 3.7 - - - -
170A VAL 2.7 36.0 + - - +
172A PRO* 4.6 13.7 - - + -
175A ALA* 3.5 31.6 - - + -
220A ARG* 6.0 3.8 - - - -
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Residues in contact with PRO 160 (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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138A ILE* 4.2 9.2 - - + -
139A VAL 4.0 4.0 - - - +
159A VAL* 1.3 93.2 - - + +
161A VAL* 1.3 61.6 + - - +
167A LEU* 4.0 18.8 - - + -
168A LYS 3.3 6.1 - - - +
169A LEU* 3.7 15.7 - - + -
220A ARG* 5.7 6.1 - - - -
222A GLU* 3.5 18.8 - - + +
223A PHE* 3.6 34.1 - - + -
230A ILE* 3.8 16.2 - - + -
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Residues in contact with VAL 161 (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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159A VAL* 3.8 9.6 - - + +
160A PRO* 1.3 79.0 - - - +
162A PHE* 1.3 68.6 + - - +
163A GLU* 3.1 14.2 + - + +
167A LEU* 3.7 3.3 - - - -
168A LYS* 2.7 42.2 + - - +
170A VAL* 3.3 37.0 - - + -
174A ASP 5.5 0.2 - - - +
175A ALA* 4.0 9.6 - - + -
222A GLU* 3.6 5.2 - - - +
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Residues in contact with PHE 162 (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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161A VAL* 1.3 74.6 - - - +
163A GLU* 1.3 59.9 + - - +
164A GLY 3.3 5.9 + - - +
165A ASN* 5.4 6.1 - - - +
166A LYS 3.3 6.1 - - - -
167A LEU* 3.4 34.5 - - + -
221A ARG* 3.4 47.8 - - - +
222A GLU* 2.9 34.6 + - + +
225A GLU* 3.7 13.5 - - + -
226A GLY* 3.7 27.8 - - - -
229A GLU* 4.7 4.7 - - - -
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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