Contacts of the strand formed by residues 60 - 65 (chain 2) in PDB entry 4C2M
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 60 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332 PRO* 4.8 8.7 - - + -
562 GLU* 4.0 1.2 - - - -
572 ASN* 3.1 42.3 + - - +
592 ARG* 1.3 106.5 - - - +
612 GLU* 1.3 65.0 + - - +
622 TYR* 3.2 33.0 - - + +
1002 VAL* 4.1 14.6 - - + -
1012 VAL 3.5 13.5 - - - +
1022 SER* 3.8 14.1 - - - +
1032 LYS* 3.9 4.3 - - - +
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Residues in contact with GLU 61 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542 HIS* 3.8 11.3 + - - -
552 GLY 3.7 5.8 - - - +
562 GLU* 3.5 18.8 - - - +
602 LEU* 1.3 75.6 - - - +
622 TYR* 1.3 68.0 + - - +
632 GLU* 3.3 22.9 - - - +
1002 VAL* 3.6 2.8 - - - +
1012 VAL* 2.8 43.6 + - + +
1032 LYS* 3.9 22.0 - - + +
1062 LYS* 2.9 40.2 + - - +
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Residues in contact with TYR 62 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262 PHE* 4.0 14.1 - + + -
302 PHE* 3.6 24.2 - + - -
312 ARG 4.5 1.7 + - - -
322 ALA* 3.5 18.9 - - + +
332 PRO* 3.8 2.8 - - - +
362 THR* 3.7 14.8 - - + -
382 PHE* 3.5 23.8 - + + -
532 LEU* 5.1 2.0 - - + -
542 HIS* 3.3 4.3 + - - -
552 GLY* 2.7 43.3 + - - +
562 GLU 4.4 0.2 - - - -
572 ASN* 3.2 28.3 + - - -
602 LEU* 3.2 35.7 - - + +
612 GLU* 1.3 77.8 - - - +
632 GLU* 1.3 64.6 + - - +
992 LYS 3.6 4.0 - - - +
1002 VAL* 3.6 27.9 - - + +
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Residues in contact with GLU 63 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532 LEU* 3.3 12.6 - - - +
542 HIS* 3.3 24.7 + - + -
612 GLU* 3.3 25.9 - - - +
622 TYR* 1.3 80.1 - - - +
642 GLY* 1.3 59.3 + - - +
982 SER* 3.1 6.2 - - - -
992 LYS* 2.9 57.9 + - - +
1012 VAL* 4.2 10.8 - - - +
1062 LYS* 5.4 1.8 + - - -
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Residues in contact with GLY 64 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522 VAL* 3.4 6.4 - - - +
532 LEU* 2.6 46.1 + - - +
632 GLU* 1.3 77.7 - - - +
652 TYR* 1.3 61.0 + - - +
962 LEU* 4.1 4.3 - - - -
972 VAL 3.2 11.7 - - - -
982 SER* 3.9 8.5 - - - -
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Residues in contact with TYR 65 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512 PHE 3.8 6.5 - - - +
522 VAL* 4.4 12.8 - - + -
642 GLY* 1.3 73.9 - - - +
662 THR* 1.3 69.3 + - - +
672 ASP* 3.8 2.8 + - + -
962 LEU* 3.2 5.6 - - - -
972 VAL* 2.7 75.3 + - + +
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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
------------------------------------------------------------
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