Contacts of the strand formed by residues 696 - 701 (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 GLY 696 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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626A THR* 4.2 1.1 - - - -
627A LEU 3.2 7.6 - - - -
628A ILE* 3.8 4.7 - - - -
656A VAL* 3.2 28.2 - - - +
657A VAL* 3.7 11.7 - - - +
663A LEU* 3.5 24.3 - - - +
695A ALA* 1.3 76.8 - - - +
697A LEU* 1.3 66.5 + - - +
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Residues in contact with LEU 697 (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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626A THR* 3.4 5.6 - - - +
627A LEU* 2.9 42.2 + - + +
629A VAL* 3.8 28.9 - - + -
643A LEU* 4.3 4.5 - - + -
645A VAL* 3.5 37.0 - - + -
653A PHE* 4.7 7.6 - - + -
655A GLY 3.9 2.0 - - - -
656A VAL* 4.4 5.4 - - + -
666A LEU* 5.0 3.8 - - + -
668A CYS* 3.7 29.6 - - - -
679A VAL* 4.9 2.7 - - + -
681A CYS* 4.4 0.7 - - - -
695A ALA* 5.2 0.2 - - + -
696A GLY* 1.3 82.9 - - - +
698A ARG* 1.3 61.2 + - - +
699A PHE* 3.4 25.4 - - + -
715A LEU* 5.0 0.2 - - + -
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Residues in contact with ARG 698 (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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624A PRO* 5.8 5.9 - - - +
625A LEU 3.4 5.3 + - - +
626A THR* 3.6 20.1 + - - +
653A PHE* 3.6 8.5 - - - -
654A ILE* 2.9 57.4 + - + +
655A GLY 3.0 15.5 + - - +
656A VAL 3.2 19.6 + - - +
657A VAL* 4.3 9.4 + - + +
659A ASN* 3.0 41.6 + - - +
697A LEU* 1.3 71.2 - - - +
699A PHE* 1.3 61.7 + - - +
557B TYR* 4.8 9.0 + - - -
2I NDG 5.2 10.3 - - - +
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Residues in contact with PHE 699 (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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624A PRO* 3.8 2.6 - - - +
625A LEU* 2.7 51.0 + - + +
627A LEU* 4.0 16.2 - - + -
645A VAL* 4.3 3.4 - - + -
647A ILE* 3.4 25.6 - - + -
651A ALA* 4.8 1.3 - - + -
652A ASP 2.9 30.5 - - - +
653A PHE* 3.8 19.1 - + + -
654A ILE* 4.0 7.9 - - - +
679A VAL* 3.5 27.8 - - + -
697A LEU* 3.4 34.3 - - + -
698A ARG* 1.3 73.4 - - - +
700A SER* 1.3 65.2 + - - +
713A PHE* 3.7 26.0 - + + -
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Residues in contact with SER 700 (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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622A ASP* 3.2 30.4 + - - +
623A ASN 3.2 15.6 + - - -
624A PRO* 4.4 1.9 - - - +
650A GLN 3.6 2.4 - - - +
651A ALA* 3.6 2.2 - - - -
652A ASP* 3.2 28.9 + - - +
654A ILE* 4.6 12.6 - - - -
699A PHE* 1.3 79.8 - - - +
701A VAL* 1.3 60.4 + - - +
702A HIS* 3.6 12.3 - - - -
1I NAG 5.2 8.0 - - - +
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Residues in contact with VAL 701 (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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617A ILE* 3.4 40.2 - - + -
621A ASP 3.3 2.6 - - - +
623A ASN* 3.2 33.5 + - + +
625A LEU* 4.9 13.9 - - + -
648A PRO* 6.1 0.2 - - + -
650A GLN* 3.3 35.2 - - + +
651A ALA* 4.2 7.4 - - + +
700A SER* 1.3 72.3 - - - +
702A HIS* 1.3 71.5 + - - +
703A GLN* 3.7 8.3 - - - +
711A VAL* 4.5 13.0 - - + -
713A PHE* 6.1 1.1 - - + -
736A LEU* 6.0 0.9 - - + -
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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