Contacts of the strand formed by residues 6 - 12 (chain B) in PDB entry 3IML
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 LEU 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A THR* 4.4 19.7 - - + +
313A SER* 3.7 27.8 + - - -
315A MET* 5.8 2.6 - - - +
5B TYR* 1.3 79.8 - - - +
7B PHE* 1.3 60.8 + - - +
173B THR* 3.8 13.0 - - + -
174B VAL 3.5 0.9 - - - -
175B ARG* 3.8 36.6 - - + +
185B ASP* 3.8 38.1 - - + +
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Residues in contact with PHE 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 4.0 11.9 - - + -
127A PHE* 4.0 17.3 - + - -
301A GLN* 5.7 5.2 - - + -
313A SER* 5.4 0.2 - - - -
5B TYR* 4.1 18.6 - + + -
6B LEU* 1.3 74.3 - - - +
8B THR* 1.3 88.2 + - - +
9B SER* 3.8 12.6 - - - -
141B PRO* 3.9 16.9 - - + +
172B VAL 3.8 0.9 - - - +
173B THR* 3.3 0.5 - - - -
174B VAL* 2.7 40.5 + - - +
176B TYR* 4.0 20.6 - + + -
256B GLY 4.2 1.3 - - - -
257B GLY 3.4 32.1 - - - -
258B ALA* 3.9 11.7 - - + -
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Residues in contact with THR 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLY 5.7 0.2 - - - -
125A LEU* 3.3 36.4 - - + +
303A SER* 3.9 25.4 + - - -
313A SER* 4.8 0.3 + - - -
7B PHE* 1.3 79.5 - - - +
9B SER* 1.3 68.9 + - - +
171B GLN* 3.4 45.5 - - + +
172B VAL 3.4 3.8 - - - +
173B THR* 2.8 30.4 + - - +
256B GLY 4.0 0.2 - - - +
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Residues in contact with SER 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 5.9 1.1 - - - -
7B PHE* 3.8 5.2 - - - -
8B THR* 1.3 75.1 + - - +
10B GLU* 1.3 61.8 - - - +
141B PRO* 3.6 15.5 - - - +
142B ILE* 3.5 33.4 + - - +
145B SER* 3.6 3.1 - - - -
171B GLN* 3.3 8.3 - - - +
172B VAL 3.0 29.7 + - - -
255B TYR 4.5 0.9 + - - -
256B GLY* 2.5 28.4 + - - -
258B ALA* 5.9 0.2 - - - +
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLN* 3.5 32.3 + - - +
124A GLY* 3.8 17.9 - - - -
125A LEU 5.4 0.9 - - - -
262A GLY 4.6 14.1 - - - +
263A GLY* 5.5 2.9 - - - -
9B SER* 1.3 77.2 - - - +
11B SER* 1.3 62.6 + - - +
12B VAL* 5.9 0.7 - - - -
142B ILE* 3.1 20.8 - - - +
145B SER* 3.8 5.2 - - - -
169B LYS* 4.8 9.1 - - - -
170B SER 3.3 13.9 - - - +
171B GLN* 4.5 3.3 + - + -
249B LYS* 5.0 9.4 - - - +
251B ILE* 6.5 0.9 - - + -
252B VAL* 3.3 27.5 - - + +
256B GLY* 5.0 2.7 + - - -
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Residues in contact with SER 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 1.3 75.3 - - - +
12B VAL* 1.3 82.7 + - - +
145B SER* 3.5 31.9 - - - -
146B HIS* 2.8 29.1 + - - -
149B VAL* 3.6 4.8 - - - +
169B LYS* 3.6 3.1 - - - +
170B SER* 3.0 31.8 + - - +
252B VAL* 3.8 9.4 - - - +
361B TYR* 4.9 0.5 - - - -
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 5.8 2.2 - - + +
11B SER* 1.3 86.7 + - - +
13B SER* 1.3 63.1 + - - +
16B HIS* 3.6 35.0 - - + +
19B LYS* 3.4 33.3 - - + +
149B VAL* 3.5 14.1 - - - +
168B ALA 3.3 7.0 - - - +
169B LYS* 4.1 15.9 - - + -
249B LYS* 4.1 27.4 - - + -
252B VAL* 4.3 6.1 - - + +
361B TYR* 4.2 9.5 + - - -
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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