Contacts of the strand formed by residues 125 - 131 (chain A) in PDB entry 2D4H
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 THR 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A VAL 2.8 6.1 + - - -
41A VAL* 3.5 21.3 - - + -
42A ALA 3.1 25.6 + - - -
123A SER* 3.2 9.0 - - - -
124A SER* 1.3 79.2 + - - +
126A PHE* 1.3 64.7 + - - +
127A VAL* 4.0 12.1 - - + -
176A PRO* 4.0 0.4 - - - -
177A ASP* 3.9 22.2 + - + +
179A VAL* 4.4 11.9 - - + -
272A TYR* 6.2 0.7 - - + -
273A ILE* 4.5 2.7 - - + -
276A ASN* 5.7 0.2 + - - -
277A SER* 2.8 38.5 + - - +
278A LYS 4.7 0.2 + - - -
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Residues in contact with PHE 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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42A ALA* 4.1 2.0 - - + -
44A VAL* 3.3 36.3 - - + -
116A PHE* 3.5 24.7 - + - -
120A VAL* 3.7 23.8 - - + -
123A SER* 4.3 3.8 - - - +
125A THR* 1.3 73.7 - - - +
127A VAL* 1.3 61.7 + - - +
128A TYR* 4.2 4.5 - - + -
142A LEU* 3.8 17.0 - - + -
145A VAL* 5.8 0.9 - - + -
176A PRO* 3.7 16.2 - - + -
177A ASP 2.7 16.0 + - - +
178A PHE* 3.4 31.0 - + - -
179A VAL* 2.7 32.7 + - - +
230A PHE* 3.9 24.5 - + - -
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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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41A VAL* 3.8 26.2 - - + -
42A ALA 2.9 15.3 + - - +
43A ILE* 3.6 21.8 - - + +
44A VAL* 2.8 31.4 + - - +
54A LEU* 4.5 3.1 - - + -
125A THR* 4.0 5.8 - - + -
126A PHE* 1.3 79.4 - - - +
128A TYR* 1.3 59.8 + - - +
179A VAL* 3.2 21.1 - - + +
181A THR* 3.9 21.5 - - + +
269A PHE* 3.9 22.7 - - + -
273A ILE* 4.2 1.6 - - + -
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Residues in contact with TYR 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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44A VAL* 3.5 20.4 - - + -
45A GLY* 4.3 11.7 - - - -
46A LEU* 5.7 1.9 - - - +
116A PHE* 3.5 27.4 - + - -
126A PHE* 4.0 4.6 - - + -
127A VAL* 1.3 70.8 - - - +
129A ASN* 1.3 56.4 + - - +
130A SER* 4.1 13.6 - - - -
138A ALA* 3.4 17.4 - - + +
141A GLN* 2.6 29.6 + - - -
142A LEU* 4.0 15.7 - - + -
178A PHE* 3.7 23.6 - - + -
179A VAL 2.7 10.0 + - - +
180A TRP* 3.2 51.3 - + - -
181A THR* 2.8 31.7 + - - -
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Residues in contact with ASN 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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43A ILE* 4.7 3.6 - - + -
44A VAL 2.8 16.3 + - - +
45A GLY* 3.5 18.9 - - - -
46A LEU 4.0 5.4 + - - -
49A THR* 3.1 49.7 + - - -
51A LYS* 3.6 17.9 - - + +
54A LEU* 3.7 11.3 - - + +
128A TYR* 1.3 74.6 - - - +
130A SER* 1.3 63.1 + - - +
181A THR* 2.5 23.5 + - - +
183A ARG* 2.9 27.0 + - - +
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Residues in contact with SER 130 (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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46A LEU* 6.5 0.9 - - - -
49A THR* 5.0 3.1 - - - -
128A TYR* 4.1 16.9 + - - -
129A ASN* 1.3 77.1 - - - +
131A ILE* 1.3 63.4 + - - +
132A GLY 4.9 0.3 + - - -
133A THR 5.5 1.7 + - - -
134A ILE* 5.7 0.7 - - - -
135A ASN* 5.5 3.0 + - - -
138A ALA* 5.4 3.1 - - - -
180A TRP* 3.1 27.4 + - - -
181A THR 3.1 5.5 + - - -
182A LEU* 3.4 12.0 - - - +
183A ARG* 2.8 33.5 + - - +
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Residues in contact with ILE 131 (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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48A ARG 3.9 8.1 - - - +
49A THR* 3.7 33.5 - - + +
130A SER* 1.3 80.0 + - - +
132A GLY* 1.3 73.6 + - - +
133A THR 4.1 5.7 - - - +
135A ASN* 5.4 4.5 + - - +
183A ARG* 3.6 14.1 - - + +
184A ASP* 3.6 32.5 - - + +
593A 5GP 3.9 11.4 - - - +
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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