Contacts of the strand formed by residues 123 - 129 (chain A) in PDB entry 2F24
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LEU* 4.1 20.2 - - + -
82A HIS* 4.3 10.3 - - - +
103A ILE* 3.4 8.7 - - - +
104A ALA* 2.8 41.5 + - - +
121A VAL 3.9 10.3 - - - +
122A THR* 1.3 80.1 - - - +
124A LEU* 1.3 61.8 + - - +
125A CYS* 3.8 3.3 + - - -
141A ASP* 2.9 32.4 + - - +
143A THR* 3.3 33.8 + - - +
144A ASP* 4.0 20.0 + - - -
151A TYR* 3.6 21.1 + - - -
157A PHE* 4.0 4.0 - - - -
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Residues in contact with LEU 124 (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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101A PHE* 4.9 5.6 - - + -
102A PHE 3.9 9.4 - - - +
103A ILE* 4.2 3.8 - - + -
123A ARG* 1.3 71.7 - - - +
125A CYS* 1.3 62.4 + - - +
141A ASP* 3.6 4.2 - - - +
142A LEU* 2.7 50.0 + - + -
143A THR* 2.9 17.7 + - - +
146A ALA* 3.9 27.4 - - + -
147A ILE* 4.8 1.8 - - + -
157A PHE* 3.8 16.4 - - + -
159A VAL* 3.6 31.4 - - + -
176A VAL* 6.0 0.4 - - + -
197A PHE* 3.9 24.9 - - + -
206A TRP* 6.5 0.4 - - + -
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Residues in contact with CYS 125 (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 LEU* 3.6 40.6 - - + -
101A PHE* 3.3 9.7 - - - +
102A PHE* 2.9 53.6 + - + +
104A ALA* 4.0 15.0 - - - -
123A ARG* 4.2 5.2 - - - -
124A LEU* 1.3 81.7 - - - +
126A GLN* 1.3 63.7 + - - +
140A ARG 3.2 12.8 - - - +
141A ASP* 4.4 5.2 - - - -
142A LEU* 4.4 3.4 - - - +
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Residues in contact with GLN 126 (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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99A PHE* 3.7 16.2 - - + -
100A LEU 3.3 10.5 - - - +
101A PHE* 3.4 33.5 - - + -
102A PHE* 4.0 1.8 - - - -
125A CYS* 1.3 79.5 - - - +
127A VAL* 1.3 67.1 + - - +
128A THR* 3.6 23.0 + - - +
138A SER 4.2 0.5 - - - +
139A PRO* 3.5 0.3 - - - +
140A ARG* 2.8 67.6 + - + +
142A LEU* 3.5 21.6 - - + +
203A GLY 5.0 0.7 - - - +
206A TRP* 4.8 3.6 + - - -
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Residues in contact with VAL 127 (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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74A VAL* 4.7 0.7 - - + -
76A GLN* 3.6 29.2 - - + +
77A ALA* 3.9 12.1 - - + -
100A LEU* 2.9 52.4 + - + +
102A PHE* 4.0 2.5 - - + -
126A GLN* 1.3 80.1 - - - +
128A THR* 1.3 64.7 + - - +
136A TRP* 3.6 25.7 - - + -
137A SER* 3.6 25.1 - - - +
139A PRO* 3.7 7.9 - - + -
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Residues in contact with THR 128 (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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97A THR* 4.1 10.8 - - + -
98A LEU 3.1 9.2 - - - +
99A PHE* 3.5 38.4 - - + -
126A GLN* 3.6 16.7 + - - +
127A VAL* 1.3 77.7 - - - +
129A SER* 1.3 61.8 + - - +
130A THR* 5.8 2.0 - - - +
136A TRP* 3.4 5.3 - - - -
137A SER* 2.8 43.3 + - - -
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Residues in contact with SER 129 (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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96A GLY 4.6 0.2 - - - +
97A THR* 3.5 5.9 - - - +
98A LEU* 3.0 35.7 + - - +
128A THR* 1.3 74.4 - - - +
130A THR* 1.3 62.5 + - - +
131A ASP* 2.7 27.4 + - - -
132A HIS 4.8 0.6 + - - -
133A GLY* 2.8 28.7 + - - -
135A THR 2.8 15.6 + - - -
136A TRP* 3.7 13.5 - - - -
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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