Contacts of the strand formed by residues 4 - 12 (chain A) 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 ASP 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ASN* 1.3 77.5 - - - +
5A TYR* 1.3 66.8 + - - +
175A ARG* 2.5 52.7 + - - +
176A TYR 3.4 5.4 - - - +
177A VAL* 3.7 6.4 - - + +
327B GLU* 3.1 32.1 + - + +
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Residues in contact with TYR 5 (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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3A ASN* 3.9 33.5 + - + -
4A ASP* 1.3 81.3 + - - +
6A LEU* 1.3 75.1 + - - +
7A PHE* 4.3 10.1 - + + -
174A VAL 3.6 0.2 - - - +
175A ARG* 3.3 3.5 - - - -
176A TYR* 2.7 80.9 + + + +
179A GLY* 4.2 9.9 + - - -
315B MET* 4.1 29.2 - - + -
316B VAL 5.9 1.6 - - - +
327B GLU* 5.4 0.9 - - - +
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Residues in contact with LEU 6 (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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5A TYR* 1.3 75.9 - - - +
7A PHE* 1.3 60.4 + - - +
173A THR* 4.1 3.6 - - + -
174A VAL 3.4 1.6 - - - -
175A ARG* 3.5 37.9 - - + +
185A ASP* 4.0 28.3 - - + +
301B GLN* 4.3 1.4 - - - +
312B THR 4.4 5.2 - - - +
313B SER* 3.9 34.6 + - - -
314B VAL 4.5 11.6 + - - +
315B MET* 3.3 29.2 + - - +
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Residues in contact with PHE 7 (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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5A TYR* 4.3 8.7 - + + -
6A LEU* 1.3 74.7 - - - +
8A THR* 1.3 72.0 + - - +
9A SER* 3.9 11.0 - - - -
141A PRO* 4.1 18.2 - - + +
172A VAL 3.9 0.9 - - - +
173A THR* 3.5 0.2 - - - -
174A VAL* 2.7 40.1 + - - +
176A TYR* 3.9 22.9 - + + -
256A GLY 4.1 2.2 - - - -
257A GLY 3.2 30.1 - - - -
258A ALA* 3.9 13.5 - - + -
127B PHE* 3.9 12.6 - + - -
260B PRO* 6.2 0.2 - - + -
301B GLN* 3.7 23.3 - - - -
315B MET* 4.1 18.6 - - - -
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Residues in contact with THR 8 (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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7A PHE* 1.3 78.9 - - - +
9A SER* 1.3 69.3 + - - +
171A GLN* 3.4 34.5 - - + -
172A VAL 3.4 6.3 - - - +
173A THR* 2.8 28.8 + - - +
256A GLY 3.7 0.7 - - - +
125B LEU* 3.5 9.9 - - + +
301B GLN* 2.9 34.9 + - - -
303B SER* 3.3 15.4 + - - +
313B SER* 2.9 20.4 + - - -
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Residues in contact with SER 9 (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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7A PHE* 3.9 5.9 - - - -
8A THR* 1.3 72.4 + - - +
10A GLU* 1.3 60.2 + - - +
141A PRO* 3.7 12.6 - - - +
142A ILE* 3.5 31.1 + - - +
145A SER* 3.6 2.7 - - - -
171A GLN* 3.2 6.8 - - - +
172A VAL 3.0 29.8 + - - -
255A TYR 4.3 0.9 + - - -
256A GLY* 2.6 33.1 + - - -
125B LEU* 3.9 7.4 - - - -
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Residues in contact with GLU 10 (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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9A SER* 1.3 76.5 - - - +
11A SER* 1.3 62.5 + - - +
12A VAL* 5.3 2.7 - - - -
142A ILE* 3.4 19.2 - - - +
145A SER* 3.6 6.5 - - - -
169A LYS* 4.3 10.9 + - - -
170A SER 3.2 14.8 - - - +
171A GLN* 4.0 4.0 - - + +
249A LYS* 4.9 7.8 - - - +
252A VAL* 3.4 26.2 - - + +
256A GLY* 5.3 1.3 - - - -
123B GLN* 2.9 26.5 + - - +
124B GLY* 3.7 16.9 - - - -
125B LEU* 3.7 19.1 + - + +
262B GLY 4.1 14.3 - - - +
263B GLY* 5.7 1.0 - - - -
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Residues in contact with SER 11 (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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10A GLU* 1.3 75.8 - - - +
12A VAL* 1.3 78.8 + - - +
145A SER* 3.6 32.5 - - - -
146A HIS* 2.9 29.6 + - - -
149A VAL* 3.5 10.2 - - - +
169A LYS* 3.5 2.1 - - - +
170A SER* 2.9 31.5 + - - +
252A VAL* 3.7 9.9 - - - +
361A TYR* 4.8 0.9 - - - -
123B GLN* 4.3 1.2 + - - -
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Residues in contact with VAL 12 (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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10A GLU* 5.3 2.9 - - - -
11A SER* 1.3 89.8 + - - +
13A SER* 1.3 70.1 + - - +
16A HIS* 3.6 30.7 - - + +
19A LYS* 3.5 34.9 - - + +
149A VAL* 3.7 10.5 - - - +
168A ALA 3.4 7.4 - - - +
169A LYS* 4.2 13.0 - - + -
249A LYS* 3.9 29.2 - - + -
252A VAL* 4.3 6.5 - - + +
361A TYR* 4.1 8.8 + - - -
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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