Contacts of the strand formed by residues 623 - 633 (chain A) in PDB entry 1L5G
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 ASN 623 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616A LYS 5.1 0.2 - - - +
617A ILE* 3.7 26.8 - - + +
618A TYR* 3.1 52.1 + - - +
621A ASP* 3.2 29.3 + - - +
622A ASP* 1.3 72.1 - - - +
624A PRO* 1.3 70.4 - - + +
625A LEU* 3.5 3.1 + - - +
700A SER* 3.2 23.0 - - - -
701A VAL* 3.2 14.5 + - + +
702A HIS 5.2 1.0 + - - -
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Residues in contact with PRO 624 (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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614A GLN* 5.6 6.4 - - - +
617A ILE* 5.1 2.9 - - - +
621A ASP* 5.2 0.2 - - - +
622A ASP 3.6 8.0 - - - +
623A ASN* 1.3 87.0 - - + +
625A LEU* 1.3 60.7 + - - +
626A THR* 5.5 0.2 - - - -
654A ILE* 5.9 0.7 - - + -
698A ARG* 5.8 5.4 - - - +
699A PHE 3.8 4.9 - - - +
700A SER* 4.7 2.5 - - - +
2I NDG 4.2 45.1 - - + +
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Residues in contact with LEU 625 (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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613A ASP 5.0 4.3 - - - +
614A GLN* 5.0 10.1 - - + +
617A ILE* 4.5 20.4 - - + -
623A ASN 4.2 4.0 - - - +
624A PRO* 1.3 75.2 - - - +
626A THR* 1.3 70.0 + - - +
627A LEU* 4.1 16.6 - - + -
697A LEU 3.6 0.5 - - - +
698A ARG* 3.4 2.5 - - - +
699A PHE* 2.7 55.1 + - + +
700A SER* 5.1 0.4 - - - -
701A VAL* 4.9 11.0 - - + -
711A VAL* 6.4 0.2 - - + -
713A PHE* 3.5 38.8 - - + -
734A VAL* 4.3 24.0 - - + -
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Residues in contact with THR 626 (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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611A ASP 5.3 1.4 - - - +
613A ASP* 4.2 32.6 + - - +
614A GLN* 6.4 0.2 - - - +
624A PRO 5.5 0.3 - - - -
625A LEU* 1.3 81.7 + - - +
627A LEU* 1.3 78.8 + - - +
628A ILE* 4.0 18.6 + - + +
657A VAL* 4.6 9.4 - - + -
663A LEU* 5.4 0.4 - - + -
696A GLY* 4.2 4.0 - - - -
697A LEU 3.4 15.0 - - - +
698A ARG* 3.6 24.9 + - + +
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Residues in contact with LEU 627 (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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610A VAL* 4.4 11.7 - - + -
611A ASP 5.2 1.3 - - - +
625A LEU* 4.1 21.3 - - + -
626A THR* 1.3 79.2 - - - +
628A ILE* 1.3 61.7 + - - +
629A VAL* 3.5 4.3 + - + -
645A VAL* 4.7 7.4 - - + -
695A ALA 3.6 0.2 - - - +
696A GLY* 3.2 6.6 - - - -
697A LEU* 2.9 43.2 + - + +
699A PHE* 4.0 19.5 - - + -
713A PHE* 3.7 41.3 - - + -
715A LEU* 5.0 6.7 - - + -
732A HIS* 3.9 29.4 - - + +
734A VAL* 5.4 0.4 - - + -
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Residues in contact with ILE 628 (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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610A VAL* 3.4 26.7 - - - +
611A ASP* 3.5 25.3 + - + +
613A ASP* 4.9 16.6 - - + +
626A THR* 4.0 12.5 + - + +
627A LEU* 1.3 76.3 - - - +
629A VAL* 1.3 63.0 + - - +
630A LYS* 5.3 0.8 - - - +
663A LEU* 3.6 31.6 - - + -
694A LEU* 4.2 24.0 - - + -
696A GLY* 3.8 8.1 - - - -
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Residues in contact with VAL 629 (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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608A VAL* 5.4 2.7 - - + -
609A SER 3.4 7.6 - - - +
610A VAL* 4.7 3.4 - - + -
627A LEU* 3.5 4.5 + - + +
628A ILE* 1.3 75.8 - - - +
630A LYS* 1.3 65.4 + - - +
631A ALA* 5.2 2.5 - - + +
643A LEU* 4.0 26.0 - - + -
666A LEU* 4.7 4.5 - - + -
694A LEU* 3.3 29.4 - - - +
695A ALA* 2.9 34.8 + - + +
697A LEU* 3.8 29.8 - - + -
715A LEU* 4.2 20.2 - - + -
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Residues in contact with LYS 630 (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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607A GLU 3.1 14.6 - - - +
608A VAL* 4.8 1.7 - - - +
609A SER* 2.9 42.8 + - - +
611A ASP* 5.8 2.0 + - - -
628A ILE* 5.3 0.9 - - + +
629A VAL* 1.3 77.3 - - - +
631A ALA* 1.3 58.1 + - - +
632A GLN* 3.7 29.0 + - + +
692A GLN* 4.6 14.9 + - + +
693A LEU 3.3 14.8 - - - +
694A LEU* 3.7 23.6 - - + +
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Residues in contact with ALA 631 (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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607A GLU 3.8 4.3 - - - -
608A VAL* 5.1 1.8 - - + +
629A VAL* 5.2 1.9 - - + +
630A LYS* 1.3 71.5 - - - +
632A GLN* 1.3 62.0 + - - +
643A LEU* 5.5 8.3 - - + -
666A LEU* 6.3 0.7 - - + -
683A LEU* 3.5 38.8 - - + -
687A MET* 3.9 3.1 - - + +
691A THR 3.6 4.0 - - - +
693A LEU* 3.0 38.6 + - + +
717A ILE* 3.9 10.8 - - + -
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Residues in contact with GLN 632 (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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606A LEU* 3.3 6.1 - - - +
607A GLU* 3.1 57.9 + - + +
609A SER* 4.7 5.9 - - - -
630A LYS* 3.7 32.2 + - + +
631A ALA* 1.3 78.4 - - - +
633A ASN* 1.3 59.3 - - - +
634A GLN* 3.3 22.7 + - - +
687A MET* 3.6 7.2 - - - +
691A THR 3.3 6.5 - - - +
692A GLN* 3.9 29.1 + - + -
717A ILE* 4.1 1.0 - - - +
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Residues in contact with ASN 633 (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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604A PRO* 3.2 13.2 - - - +
605A LYS 3.2 11.6 + - - +
606A LEU* 3.9 8.2 - - + +
632A GLN* 1.3 74.4 - - - +
634A GLN* 1.3 56.1 + - - +
635A GLY 3.5 2.2 + - - -
636A GLU 2.9 27.1 + - - +
638A ALA* 3.5 9.1 - - - +
687A MET* 2.6 46.9 + - + +
688A LYS 3.4 12.4 + - - +
690A GLY* 2.7 37.2 + - - -
691A THR 3.2 6.1 + - - +
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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