Contacts of the strand formed by residues 702 - 709 (chain B) in PDB entry 3LMG
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 GLY 702 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ANP 4.1 5.2 - - - -
698B SER* 3.2 19.4 - - - -
699B GLY 3.2 12.4 + - - +
700B VAL 3.9 0.2 - - - -
701B PHE* 1.3 81.4 - - - +
703B THR* 1.3 64.5 + - - -
723B LYS* 4.0 13.8 - - - +
724B VAL 3.2 14.1 - - - -
725B ILE* 4.4 1.3 - - - -
728B LYS* 5.7 1.1 - - - +
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Residues in contact with THR 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A LYS* 6.0 0.3 - - - +
695A VAL* 4.3 0.4 - - + -
705A HIS* 3.6 32.4 - - + -
695B VAL* 3.7 15.0 - - + -
697B GLY 3.8 7.4 - - - +
698B SER* 3.9 7.8 - - - -
702B GLY* 1.3 77.1 + - - -
704B VAL* 1.3 66.0 + - - +
705B HIS* 3.5 25.9 - - - +
722B ILE 3.4 2.1 - - - +
723B LYS* 3.1 2.4 - - - +
724B VAL* 2.6 44.5 + - - +
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Residues in contact with VAL 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ANP 3.3 55.9 - - + +
695B VAL* 3.5 3.3 - - - +
696B LEU* 2.9 27.6 + - + +
697B GLY 2.9 16.5 + - - +
703B THR* 1.3 76.1 - - - +
705B HIS* 1.3 60.9 + - - +
721B CYS* 3.2 35.0 - - - -
722B ILE 3.3 6.7 - - - +
723B LYS* 3.8 25.4 - - + -
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Residues in contact with HIS 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A SER* 5.4 0.4 + - - -
703A THR* 3.5 29.5 + - + -
705A HIS* 5.0 1.7 + - - -
692B LYS* 3.9 38.0 - - + +
694B LYS 3.3 8.2 - - - +
695B VAL* 3.4 31.9 + - + +
696B LEU* 4.4 3.6 - - - -
703B THR* 3.5 29.9 - - + +
704B VAL* 1.3 74.5 - - - +
706B LYS* 1.3 63.5 + - - +
707B GLY 3.3 0.7 + - - -
721B CYS* 3.7 2.9 - - - -
722B ILE* 2.7 40.3 + - + +
724B VAL* 4.0 18.8 - - + +
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Residues in contact with LYS 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B LYS* 4.2 0.2 - - - -
693B LEU* 2.9 40.2 + - + +
694B LYS* 2.6 28.6 + - + +
696B LEU* 3.8 21.6 - - + +
705B HIS* 1.3 70.2 - - - +
707B GLY* 1.3 68.8 + - - +
708B VAL* 5.3 2.2 - - - +
719B PRO* 4.4 18.0 - - - +
720B VAL 4.2 2.2 - - - -
721B CYS* 5.1 1.3 - - - +
770B TYR* 3.6 51.9 - - + +
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Residues in contact with GLY 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B ARG 3.2 14.8 - - - -
692B LYS* 4.3 0.4 - - - -
693B LEU* 4.0 6.1 - - - -
705B HIS 3.3 2.2 + - - -
706B LYS* 1.3 81.6 - - - +
708B VAL* 1.3 69.2 + - - +
719B PRO* 3.8 3.3 - - - +
720B VAL* 2.9 32.9 + - - +
722B ILE* 4.2 8.7 - - - -
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Residues in contact with VAL 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689B GLU 3.9 0.5 - - - +
690B LEU* 3.8 1.4 - - - +
691B ARG* 2.9 37.8 + - + +
693B LEU* 3.5 27.3 - - + +
706B LYS* 5.3 2.7 - - - +
707B GLY* 1.3 80.4 - - - +
709B TRP* 1.3 62.9 + - - +
710B ILE* 3.7 22.8 + - + +
717B LYS* 3.3 50.5 - - + -
718B ILE 3.3 7.4 - - - +
719B PRO* 4.7 3.8 - - + -
720B VAL* 3.7 4.8 - - - +
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Residues in contact with TRP 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683B ARG* 3.6 41.3 - - - -
685B PHE* 3.5 26.9 - + + -
689B GLU* 3.2 35.1 + - + -
690B LEU* 4.1 8.1 - - + -
708B VAL* 1.3 73.7 - - - +
710B ILE* 1.3 63.7 + - - +
711B PRO* 3.3 40.8 - - + +
716B ILE 3.4 1.0 - - - +
718B ILE* 2.8 58.0 + - + +
720B VAL* 3.5 29.5 - - + +
756B LEU* 5.1 11.7 - - + -
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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