Contacts of the strand formed by residues 136 - 144 (chain D) in PDB entry 5AFK
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 ALA 136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D ASP 4.4 2.0 - - - +
127D VAL* 4.0 22.7 - - + -
129D GLY* 3.4 3.5 + - - +
130D VAL* 3.7 27.1 - - + +
135D GLY* 1.3 74.8 - - - -
137D THR* 1.3 62.9 + - - +
199D THR* 3.2 3.5 - - - -
200D PHE* 2.7 52.1 + - + +
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Residues in contact with THR 137 (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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125D CYS* 3.4 10.6 - - - -
126D ASP* 4.3 9.2 + - - +
134D SER 5.2 0.7 + - - -
135D GLY 5.2 0.7 + - - -
136D ALA* 1.3 73.4 - - - +
138D CYS* 1.3 64.5 + - - +
139D LYS* 5.5 4.4 - - + +
197D THR* 3.5 29.8 - - + -
198D VAL 3.4 3.4 - - - +
199D THR* 3.2 26.6 + - - +
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Residues in contact with CYS 138 (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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48D VAL* 3.7 22.0 - - + -
125D CYS* 2.0 48.2 - - + -
127D VAL* 4.2 4.7 - - - -
137D THR* 1.3 76.3 - - - +
139D LYS* 1.3 63.4 + - - +
140D LEU* 4.0 10.1 - - + -
196D PHE 3.5 1.6 - - - +
197D THR* 3.3 5.2 - - - +
198D VAL* 2.9 41.6 + - + +
200D PHE* 4.0 20.2 - - + -
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Residues in contact with LYS 139 (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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92D ASN* 2.5 37.8 + - - +
124D SER 5.7 0.2 + - - -
125D CYS* 4.7 2.2 - - - +
137D THR* 5.5 4.0 - - + -
138D CYS* 1.3 75.7 - - - +
140D LEU* 1.3 58.6 + - - +
141D LYS* 3.5 2.6 + - + +
178D LYS* 6.4 0.4 - - - +
195D THR* 4.0 20.5 - - + +
196D PHE 3.8 3.1 - - - -
197D THR* 3.7 27.5 + - + +
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Residues in contact with LEU 140 (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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33D LEU* 4.3 21.1 - - + -
35D LEU* 5.5 4.0 - - + -
48D VAL* 5.3 2.9 - - + -
50D VAL* 5.0 15.3 - - + -
52D PHE* 5.8 0.7 - - + -
92D ASN* 4.2 2.5 - - - +
123D PHE* 3.7 43.7 - - + -
138D CYS* 4.6 11.0 - - + -
139D LYS* 1.3 77.9 - - - +
141D LYS* 1.3 61.4 + - - +
142D PHE* 3.7 23.6 - - + -
195D THR* 3.3 2.6 - - - -
196D PHE* 2.9 39.7 + - + +
198D VAL* 3.9 24.7 - - + -
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Residues in contact with LYS 141 (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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90D ALA* 3.5 5.0 - - - +
91D TYR* 2.8 73.2 + - + -
92D ASN* 3.3 12.9 + - - +
123D PHE* 5.2 0.6 - - - -
139D LYS* 3.5 4.7 + - + +
140D LEU* 1.3 73.2 - - - +
142D PHE* 1.3 62.2 + - - +
182D ARG* 4.5 9.0 - - - +
184D TYR* 4.0 7.5 + - - -
193D ASP* 2.9 39.3 + - + +
194D VAL 3.8 2.0 - - - -
195D THR* 3.8 19.1 - - + +
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Residues in contact with PHE 142 (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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31D PHE* 3.8 29.4 - + + -
33D LEU* 3.6 31.2 - - + -
52D PHE* 4.3 15.0 - + - -
54D LEU* 4.8 7.2 - - + -
88D LEU* 5.4 7.9 - - + -
89D ALA 3.2 20.4 - - - +
90D ALA* 3.8 19.1 - - + -
91D TYR* 4.1 1.1 - - - -
121D GLN* 4.8 1.8 - - - -
123D PHE* 4.1 20.2 - + - -
140D LEU* 3.7 22.9 - - + -
141D LYS* 1.3 75.6 - - - +
143D GLY* 1.3 57.9 + - - +
154D LEU* 3.9 2.7 - - - +
193D ASP* 3.1 6.5 - - - -
194D VAL 2.6 41.8 + - - +
196D PHE* 4.0 11.4 - + - -
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Residues in contact with GLY 143 (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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88D LEU* 3.8 7.7 - - - +
89D ALA* 3.1 26.0 + - - +
91D TYR* 3.4 18.3 - - - -
142D PHE* 1.3 74.6 - - - +
144D SER* 1.3 69.3 + - - +
145D TRP 3.4 0.5 + - - -
154D LEU* 4.0 7.9 - - - -
192D PRO 3.9 15.3 - - - -
193D ASP* 4.1 0.4 - - - -
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Residues in contact with SER 144 (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 ASP* 2.7 28.1 + - - -
88D LEU* 3.6 9.0 - - - +
91D TYR* 3.7 3.6 + - - -
143D GLY* 1.3 72.8 - - - -
145D TRP* 1.3 60.8 + - - +
147D HIS* 2.9 39.6 + - - +
152D LEU* 3.8 21.8 - - - -
154D LEU* 4.7 1.8 - - - +
191D TYR* 4.5 4.0 - - - +
192D PRO* 4.3 9.7 + - - +
1205D L0B 3.7 16.6 - - - +
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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