Contacts of the strand formed by residues 118 - 123 (chain A) in PDB entry 3SOQ
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 ARG 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A TRP* 4.0 0.6 - - - +
112A THR* 3.5 3.8 - - - -
113A ASP* 3.0 31.2 + - + +
116A THR* 3.2 38.6 + - - +
117A ASN* 1.3 76.5 - - - +
119A ILE* 1.3 65.4 + - - +
120A GLU* 3.7 28.8 + - + +
129A ARG* 5.5 0.8 - - - +
131A VAL* 4.2 30.2 - - + +
133A PHE 3.3 7.9 - - - +
134A TRP* 4.2 18.9 - - + +
137A LEU* 4.0 3.1 - - - +
140A PRO* 4.5 2.0 - - - +
312A THR* 5.6 4.8 + - - +
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Residues in contact with ILE 119 (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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110A TYR* 5.1 0.7 - - + -
111A TRP 3.4 8.7 - - - +
112A THR* 4.0 15.0 - - + -
118A ARG* 1.3 78.4 - - - +
120A GLU* 1.3 69.9 + - - +
131A VAL 3.9 0.2 - - - -
132A LEU* 2.9 30.5 + - + -
133A PHE* 2.9 28.9 + - + +
137A LEU* 4.0 13.2 - - + -
140A PRO* 5.0 1.3 - - + -
143A ILE* 4.3 16.4 - - + -
152A MET* 4.7 9.6 - - - -
154A TRP* 3.3 59.2 - - + +
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Residues in contact with GLU 120 (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 LEU 3.8 0.2 - - - +
110A TYR* 3.3 7.3 - - - +
111A TRP* 3.0 57.9 + - + +
113A ASP* 6.2 0.2 - - - +
116A THR* 5.4 0.7 + - - -
118A ARG* 3.7 28.8 + - + +
119A ILE* 1.3 80.3 - - - +
121A VAL* 1.3 62.0 + - - +
129A ARG* 3.0 44.4 + - - +
130A LYS 3.5 6.3 - - - +
131A VAL* 3.8 29.2 + - + -
132A LEU* 4.2 4.7 - - - +
312A THR* 4.8 2.1 + - - -
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Residues in contact with VAL 121 (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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108A LYS* 3.8 14.6 - - + -
109A LEU 3.1 11.7 - - - +
110A TYR* 3.6 36.6 - - + +
111A TRP* 4.0 4.5 - - - -
120A GLU* 1.3 75.2 - - - +
122A SER* 1.3 69.3 + - - +
128A LEU 3.9 0.2 - - - +
129A ARG* 3.5 1.4 - - - -
130A LYS* 2.9 50.6 + - + +
132A LEU* 3.8 20.9 - - + -
296A LEU* 4.6 3.4 - - + -
298A LEU* 4.1 20.0 - - + -
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Residues in contact with SER 122 (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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91A VAL* 4.2 0.2 - - - +
108A LYS* 3.2 13.1 - - - +
109A LEU* 2.7 40.2 + - - +
111A TRP* 3.5 18.7 - - - -
121A VAL* 1.3 77.8 - - - +
123A ASN* 1.3 69.0 + - - +
126A GLY* 3.6 18.8 - - - -
127A SER 3.6 12.6 - - - -
128A LEU 4.1 4.5 - - - -
129A ARG* 4.0 9.4 - - - -
296A LEU* 4.6 1.3 - - - -
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Residues in contact with ASN 123 (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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1A GOL 3.3 19.0 + - - +
90A VAL* 4.8 0.2 - - - +
107A GLU 4.0 2.7 - - - -
108A LYS* 2.8 33.1 + - - -
109A LEU* 4.1 4.0 - - - +
122A SER* 1.3 85.3 + - - +
124A LEU* 1.3 66.8 + - - +
125A ASP* 3.1 17.5 - - - +
126A GLY 2.9 10.9 + - - -
127A SER* 3.0 23.3 + - - +
128A LEU* 3.5 24.0 - - - +
295A HIS 5.2 1.8 + - - +
296A LEU* 3.7 7.2 - - - +
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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