Contacts of the strand formed by residues 31 - 36 (chain D) in PDB entry 5LN3
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 THR 31 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D SER* 1.4 76.2 + - - +
32D ALA* 1.4 68.6 + - - +
33D VAL* 4.5 5.4 - - + -
45D VAL* 3.5 5.2 - - - +
46D GLU* 2.9 55.7 + - - +
160D ALA* 5.8 1.6 - - + -
161D ILE 3.5 13.2 - - - +
163D ARG* 2.9 32.2 + - - +
165D ALA* 6.3 1.6 - - - -
168D VAL* 5.8 4.7 - - + -
195D LEU* 4.5 14.9 - - + +
198D VAL* 4.1 13.3 - - + +
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Residues in contact with ALA 32 (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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30D SER 4.2 0.6 - - - -
31D THR* 1.4 72.8 - - - +
33D VAL* 1.3 67.4 + - - +
44D GLY 3.4 7.9 - - - +
45D VAL* 3.8 19.3 - - + -
72D ALA* 4.9 7.2 - - + -
73D PHE 5.1 8.5 - - - +
74D ALA* 6.4 0.2 - - + -
132D LEU* 3.9 18.2 - - + -
161D ILE* 3.0 43.0 + - + +
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Residues in contact with VAL 33 (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 THR* 4.5 6.5 - - + -
32D ALA* 1.3 79.5 - - - +
34D GLY* 1.3 63.7 + - - +
35D VAL* 5.2 1.3 - - + -
42D VAL 5.6 0.2 - - - +
43D LEU* 3.6 7.4 - - - +
44D GLY* 3.1 37.0 + - - +
132D LEU* 3.8 6.5 - - - +
159D ASN 3.3 11.2 - - - +
160D ALA* 3.9 17.7 - - + +
168D VAL* 4.7 13.0 - - + -
172D LEU* 5.1 7.2 - - + -
191D VAL* 4.0 33.2 - - + +
194D ALA* 5.5 3.6 - - + -
195D LEU* 3.9 23.3 - - + -
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Residues in contact with GLY 34 (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 VAL* 1.3 77.1 - - - +
35D VAL* 1.3 67.7 + - - +
41D VAL* 5.8 0.2 - - - -
42D VAL 3.2 10.5 - - - -
43D LEU* 4.1 10.3 - - - -
132D LEU* 4.1 4.9 - - - +
134D VAL* 5.5 1.6 - - - -
144D LEU* 4.0 14.1 - - - +
158D ALA* 3.9 3.6 - - - -
159D ASN 3.0 30.4 + - - +
172D LEU* 5.2 0.2 - - - +
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Residues in contact with VAL 35 (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 VAL* 5.2 2.7 - - + +
34D GLY* 1.3 81.4 - - - +
36D ARG* 1.3 74.6 + - - +
41D VAL* 3.3 6.0 - - - +
42D VAL* 2.9 34.7 + - + +
144D LEU* 5.4 0.7 - - - -
157D LYS 4.7 4.0 - - - +
158D ALA* 5.2 4.3 - - + +
172D LEU* 5.1 9.4 - - + -
176D TYR* 3.8 29.8 - - + +
187D THR* 3.3 30.5 - - + -
191D VAL* 3.5 29.6 - - + -
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Residues in contact with ARG 36 (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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35D VAL* 1.3 86.5 - - - +
37D GLY* 1.3 63.1 + - - +
38D ARG* 5.7 1.6 - - - +
40D ILE 3.8 6.3 - - - -
41D VAL* 4.2 6.3 - - + -
141D THR* 4.7 6.1 - - - +
142D PRO* 3.2 48.8 + - + +
143D ARG* 4.7 0.2 - - - +
144D LEU* 3.8 35.2 - - + +
156D TRP 3.8 8.7 - - - -
157D LYS* 3.7 43.6 + - - +
176D TYR* 5.8 1.6 - - - -
187D THR* 5.2 0.2 - - - +
60E GLU* 6.3 0.2 - - - -
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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