Contacts of the strand formed by residues 127 - 132 (chain B) in PDB entry 4F4I
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 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B PHE 3.3 1.6 + - - -
5B ILE* 3.2 33.7 - - + +
6B THR 2.9 23.6 + - - -
125B PRO* 3.1 4.0 - - - +
126B ASP* 1.3 82.2 - - - +
128B THR* 1.3 65.0 + - - +
129B ILE* 4.1 24.0 - - + -
176B GLN 5.8 0.7 - - - +
177B ARG* 3.4 19.5 - - - +
179B LYS* 4.2 23.8 - - + -
197B THR* 4.6 2.7 - - + +
198B ILE* 4.4 8.7 - - - -
201B TYR* 3.7 42.6 - - + -
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Residues in contact with THR 128 (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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6B THR* 2.9 26.9 + - - +
8B GLU* 3.6 21.5 - - + -
95B ASP* 4.0 2.2 - - - +
125B PRO* 3.7 3.3 - - - +
127B LEU* 1.3 74.2 - - - +
129B ILE* 1.3 69.2 + - - +
130B TYR 3.8 0.3 + - - -
177B ARG* 2.6 35.2 + - - -
178B PHE* 3.3 36.2 - - + -
179B LYS 3.0 25.5 + - - +
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Residues in contact with ILE 129 (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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5B ILE* 4.4 5.4 - - + -
6B THR 2.8 11.3 + - - +
7B PHE* 3.6 27.8 - - + -
8B GLU* 3.2 24.8 + - - +
127B LEU* 4.1 17.9 - - + -
128B THR* 1.3 81.3 - - - +
130B TYR* 1.3 63.4 + - - +
131B LEU* 3.8 24.7 - - + -
179B LYS 3.5 7.0 - - - +
181B VAL* 4.7 6.5 - - + -
194B THR* 4.0 20.4 - - + +
197B THR* 3.6 33.2 - - + -
198B ILE* 4.4 11.4 - - + -
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Residues in contact with TYR 130 (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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8B GLU* 3.2 20.9 - - + -
9B GLY* 4.0 3.6 - - - -
10B PRO* 4.3 6.5 - - + +
128B THR 3.8 0.4 + - - -
129B ILE* 1.3 75.3 - - - +
131B LEU* 1.3 76.9 + - - +
132B ASN* 3.2 32.9 + - + -
133B VAL 5.2 0.9 + - - -
164B ILE* 4.3 11.1 + - - +
167B TYR* 2.9 53.2 - + + +
168B GLN* 4.4 5.6 + - - -
171B ILE* 4.0 32.3 - - + -
178B PHE* 4.5 17.9 - + + -
179B LYS 3.0 12.7 + - - +
180B SER* 3.4 13.0 - - - +
181B VAL* 3.0 26.9 + - - +
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Residues in contact with LEU 131 (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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7B PHE* 5.1 4.0 - - + -
8B GLU 3.1 18.9 + - - +
10B PRO* 3.8 11.6 - - - +
13B SER* 3.4 39.4 - - - +
14B GLY 3.9 2.0 - - - -
15B LYS* 3.3 40.8 - - + +
18B VAL* 4.2 16.4 - - + -
129B ILE* 3.8 25.1 - - + -
130B TYR* 1.3 74.5 - - - +
132B ASN* 1.3 59.7 + - - +
133B VAL 3.1 7.4 + - - -
181B VAL* 4.2 4.0 - - + -
183B ALA* 3.9 4.7 - - + -
190B VAL* 4.2 11.0 - - + -
194B THR* 4.1 13.2 - - - +
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Residues in contact with ASN 132 (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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49A LYS* 2.9 35.7 + - - +
52A LEU* 3.3 32.1 - - - +
53A GLU* 4.0 5.7 + - - +
130B TYR* 3.2 25.0 + - + +
131B LEU* 1.3 70.5 - - - +
133B VAL* 1.3 66.2 + - - +
134B SER* 5.6 0.2 - - - -
164B ILE* 5.4 0.5 - - - +
168B GLN* 3.3 21.3 + - - +
180B SER* 4.7 4.9 + - - -
181B VAL 3.1 17.5 + - - +
183B ALA 2.6 28.9 + - - -
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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