Contacts of the strand formed by residues 124 - 129 (chain D) in PDB entry 4PEI
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 124 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D GLN* 3.7 24.5 - - - +
9D ILE* 3.5 31.9 - - + -
39D PHE* 4.2 9.2 - - + -
119D ILE 3.7 0.2 - - - +
120D ASN* 3.4 8.0 - - - +
121D ILE 2.8 34.5 + - - +
122D ASN 4.0 0.4 - - - +
123D GLY* 1.3 83.9 - - - +
125D ARG* 1.3 63.5 + - - +
126D ILE* 4.0 10.3 + - + +
175D ASP* 3.3 31.0 - - + +
176D ILE* 4.5 6.5 - - + -
261D LEU* 4.1 17.5 - - + -
262D PRO 5.0 3.6 - - - +
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Residues in contact with ARG 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D CYS* 4.1 8.9 - - - -
119D ILE 3.6 3.1 - - - -
120D ASN* 3.8 14.1 - - - +
123D GLY 5.2 2.2 - - - +
124D LEU* 1.3 75.3 - - - +
126D ILE* 1.3 60.6 + - - +
168D LEU* 2.9 34.9 + - - +
171D SER* 5.7 0.2 - - - -
172D SER* 3.0 47.7 + - - +
173D GLN 3.5 10.1 - - - +
174D ILE* 3.6 21.1 - - + +
175D ASP* 2.6 38.5 + - - +
176D ILE 3.3 5.5 + - - -
272D ASP* 2.9 35.5 + - - -
274D ASP* 3.6 18.9 + - - +
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Residues in contact with ILE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D PHE* 3.9 33.9 - - + -
41D ILE* 4.3 4.7 - - + -
85D LEU* 4.5 5.6 - - + -
113D LEU* 4.3 5.7 - - + +
117D SER 4.0 0.2 - - - +
118D CYS* 3.1 2.7 - - - -
119D ILE* 2.7 54.2 + - + +
121D ILE* 4.0 11.9 - - + -
124D LEU* 4.4 11.4 - - + -
125D ARG* 1.3 78.8 - - - +
127D VAL* 1.3 72.7 + - - +
176D ILE* 3.2 35.2 - - + +
178D LEU* 4.0 20.9 - - + -
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 4.2 3.1 - - - -
117D SER 3.2 7.6 - - - +
118D CYS* 3.9 22.2 - - + -
126D ILE* 1.3 78.3 - - - +
128D GLY* 1.3 71.1 + - - +
129D VAL* 4.3 2.0 - - + -
165D LEU* 4.1 21.1 - - + -
168D LEU* 4.1 6.7 - - + -
174D ILE* 3.9 26.7 - - + +
176D ILE 2.8 8.5 + - - +
177D SER* 3.3 19.6 - - - +
178D LEU* 2.9 26.3 + - - +
217D ILE* 5.2 0.7 - - + -
221D LEU* 4.0 16.8 - - + -
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Residues in contact with GLY 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ILE* 3.5 22.9 - - - -
113D LEU* 3.7 12.6 - - - +
116D CYS* 3.2 29.0 - - - +
117D SER 2.9 10.9 + - - +
127D VAL* 1.3 75.5 - - - +
129D VAL* 1.3 64.6 + - - +
130D SER 4.2 0.2 - - - -
178D LEU* 3.5 4.5 - - - -
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Residues in contact with VAL 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ILE* 3.4 6.6 - - - +
115D VAL 4.0 5.2 - - - +
127D VAL* 4.3 7.2 - - + -
128D GLY* 1.3 78.4 - - - +
130D SER* 1.3 70.5 + - - +
131D GLY 4.7 0.5 - - - +
157D THR* 4.2 7.4 - - + -
161D VAL* 4.0 26.5 - - + -
165D LEU* 3.8 21.3 - - + -
177D SER* 4.6 0.2 - - - +
178D LEU 2.8 15.7 + - - +
179D SER* 3.4 20.1 - - - -
180D HIS 3.9 1.7 + - - -
213D ILE* 5.0 0.2 - - + -
214D ASN* 3.5 26.9 + - - +
217D ILE* 4.0 9.4 - - + -
226D TRP* 4.5 10.3 - - + -
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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