Contacts of the strand formed by residues 702 - 709 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A ANP 4.0 6.3 - - - -
698A SER* 3.3 6.4 - - - -
699A GLY 3.1 25.4 + - - +
701A PHE* 1.3 82.9 - - - +
703A THR* 1.3 63.3 + - - -
723A LYS* 3.9 16.4 - - - +
724A VAL 3.1 14.6 - - - -
725A ILE* 4.3 1.8 - - - -
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Residues in contact with THR 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695A VAL* 3.9 9.2 - - + -
697A GLY 3.6 15.0 - - - +
698A SER* 3.8 10.6 - - - -
702A GLY* 1.3 76.5 + - - -
704A VAL* 1.3 59.6 + - - +
705A HIS* 3.4 31.0 - - - +
723A LYS* 3.4 1.6 - - - +
724A VAL* 2.8 41.8 + - - +
692B LYS* 5.9 0.5 - - - +
695B VAL* 4.0 1.3 - - + -
705B HIS* 3.5 31.2 + - + -
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Residues in contact with VAL 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ANP 3.1 63.5 - - + +
695A VAL* 3.6 3.3 - - - +
696A LEU* 2.9 26.8 + - + +
697A GLY 2.8 14.5 + - - +
703A THR* 1.3 71.7 - - - +
705A HIS* 1.3 61.4 + - - +
721A CYS* 3.2 34.8 - - + -
722A ILE 3.6 6.1 - - - +
723A LYS* 3.8 26.5 - - + +
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Residues in contact with HIS 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A LYS* 3.9 34.7 + - + +
694A LYS 3.3 6.4 + - - +
695A VAL* 3.2 35.6 + - + +
696A LEU* 4.6 0.2 - - - -
703A THR* 3.4 34.5 - - - +
704A VAL* 1.3 75.8 - - - +
706A LYS* 1.3 65.2 + - - +
721A CYS* 3.5 6.8 - - - -
722A ILE* 2.6 45.6 + - - +
724A VAL* 4.2 14.9 - - + +
698B SER* 5.3 0.6 + - - -
703B THR* 3.6 27.4 + - + +
705B HIS* 5.0 1.6 + - - -
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Residues in contact with LYS 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A LYS* 3.8 1.0 - - - -
693A LEU* 2.8 34.4 + - + +
694A LYS* 2.6 39.9 + - + +
696A LEU* 4.0 22.0 - - + +
705A HIS* 1.3 71.3 - - - +
707A GLY* 1.3 70.3 + - - +
708A VAL* 5.5 2.6 - - - +
719A PRO* 4.4 18.8 - - - +
720A VAL 4.0 3.6 - - - +
721A CYS* 4.9 1.6 - - - +
770A TYR* 3.6 51.9 - - + +
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Residues in contact with GLY 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691A ARG 3.1 12.8 - - - -
692A LYS* 4.1 2.2 - - - -
693A LEU* 3.6 12.0 - - - +
705A HIS 3.5 1.2 + - - -
706A LYS* 1.3 82.0 + - - +
708A VAL* 1.3 65.3 + - - +
719A PRO* 3.7 2.6 - - - +
720A VAL* 2.9 35.2 + - - +
722A ILE* 4.2 7.9 - - - -
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Residues in contact with VAL 708 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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689A GLU 3.9 0.2 - - - +
690A LEU* 3.7 3.3 - - - +
691A ARG* 2.7 34.1 + - + +
693A LEU* 3.3 24.4 - - + +
706A LYS* 5.5 3.4 - - - +
707A GLY* 1.3 77.2 - - - +
709A TRP* 1.3 68.1 + - - +
710A ILE* 3.6 29.2 - - + -
717A LYS* 3.6 40.2 - - + -
718A ILE 3.3 9.0 - - - +
719A PRO* 4.8 2.5 - - + -
720A VAL* 3.7 6.2 - - - +
722A ILE* 4.6 0.2 - - - +
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Residues in contact with TRP 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683A ARG* 3.7 22.9 - - - -
685A PHE* 3.3 29.6 - + - -
689A GLU* 3.1 47.2 + - + +
690A LEU* 3.8 13.7 - - + -
708A VAL* 1.3 76.6 - - - +
710A ILE* 1.3 63.9 + - - +
711A PRO* 3.3 36.8 - - + +
716A ILE 3.8 3.6 - - - +
718A ILE* 2.7 67.2 + - + +
720A VAL* 3.9 18.8 - - + -
756A LEU* 6.1 4.3 - - + -
767A VAL* 5.9 0.4 - - + -
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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