Contacts of the strand formed by residues 116 - 122 (chain D) in PDB entry 4PRO
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 VAL 116 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B ASN* 3.0 27.1 - - - +
113D LEU* 3.5 31.0 - - + +
114D ASP 3.2 4.6 - - - +
115D GLY* 1.3 80.5 + - - +
117D GLN* 1.3 62.6 + - - +
118D SER 4.1 0.4 - - - +
119D TRP* 3.5 35.2 - - + -
130D VAL* 4.1 9.6 - - + -
131D LYS 3.8 9.2 - - - +
132D VAL* 4.2 11.2 - - + -
133D ASP* 5.2 0.2 - - - -
139D ALA 4.2 19.1 - - - +
140D GLY* 4.5 0.7 - - - -
143D PHE* 4.2 11.4 - - + -
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Residues in contact with GLN 117 (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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122B ASN* 3.1 23.9 + - - +
162B ASN* 3.9 7.9 - - - +
178B SER* 4.9 4.0 - - - -
115D GLY 3.7 0.8 + - - -
116D VAL* 1.3 72.3 - - - +
118D SER* 1.3 65.7 + - - +
131D LYS* 2.7 25.5 + - + +
133D ASP* 3.1 33.1 + - - +
159D SER* 2.6 49.6 + - - -
160D PRO 3.5 3.8 + - - -
161D GLY 3.4 13.1 + - - -
163D LEU* 3.3 39.0 - - + +
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Residues in contact with SER 118 (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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119B VAL* 4.0 16.0 - - - +
120B THR 3.0 20.6 - - - -
121B ALA* 4.1 4.5 - - - -
178B SER* 4.7 7.8 + - - -
180B LEU* 5.5 3.2 - - - +
116D VAL* 3.8 1.4 - - - +
117D GLN* 1.3 84.0 + - - +
119D TRP* 1.3 75.1 + - - +
120D TYR* 4.4 4.2 - - - -
130D VAL* 3.4 2.1 - - - +
131D LYS* 2.7 48.5 + - - +
163D LEU* 5.0 3.7 - - - +
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Residues in contact with TRP 119 (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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119B VAL* 3.8 0.3 - - - -
120B THR* 3.0 51.1 + - + -
122B ASN* 4.0 22.2 - - + -
127B ALA* 5.6 1.1 - - + -
95D MET* 3.7 19.8 - - - +
98D LEU* 3.8 29.3 - - + +
99D ASP* 3.2 18.6 + - - +
102D ALA* 3.7 31.0 - - + -
113D LEU* 4.2 9.0 - - + -
116D VAL* 3.5 27.6 - - + -
118D SER* 1.3 95.1 - - - +
120D TYR* 1.3 67.1 + - - +
128D VAL* 4.7 0.4 - - + -
129D VAL 2.9 14.6 - - - +
130D VAL* 3.9 14.1 - - + -
143D PHE* 3.8 17.5 - + - -
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Residues in contact with TYR 120 (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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115B THR 5.2 0.2 - - - -
116B ALA* 3.5 24.0 - - + -
117B LYS 4.3 2.2 - - - +
118B ASN 4.0 3.8 - - - +
119B VAL* 3.8 35.7 - - + -
133B GLN* 3.3 26.9 + - - -
95D MET* 3.7 10.9 - - - -
118D SER* 4.4 4.0 - - - -
119D TRP* 1.3 83.3 - - - +
121D VAL* 1.3 72.7 + - - +
122D ASP* 3.9 20.5 - - + -
128D VAL* 3.4 7.2 - - - +
129D VAL* 2.8 53.0 + - + +
131D LYS* 3.3 32.8 + - + -
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Residues in contact with VAL 121 (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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116B ALA* 4.8 2.9 - - - +
117B LYS 4.5 9.3 + - - +
118B ASN* 5.1 2.8 + - + +
88D LEU* 3.7 28.7 - - + -
91D LEU* 3.9 29.8 - - + +
92D GLN* 4.1 18.2 - - - +
95D MET* 3.7 31.9 - - + +
120D TYR* 1.3 81.6 - - - +
122D ASP* 1.3 61.2 + - - +
123D PRO* 3.4 18.1 - - + +
127D ALA 4.0 3.6 - - - -
128D VAL* 4.3 4.5 - - + +
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Residues in contact with ASP 122 (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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115B THR 4.4 12.5 - - - +
116B ALA* 5.4 0.6 - - - +
120D TYR* 3.4 12.9 + - + -
121D VAL* 1.3 75.7 - - - +
123D PRO* 1.3 68.2 - - - +
124D ARG* 3.6 18.1 + - - +
125D SER* 2.9 35.5 + - - +
126D ASN 3.0 8.0 + - - -
127D ALA 2.8 22.5 + - - +
129D VAL* 3.7 24.1 - - + +
155D ARG* 3.9 4.0 + - - -
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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