Contacts of the strand formed by residues 713 - 721 (chain I) in PDB entry 3AOI
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 ILE 713 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1032H PHE* 4.7 4.3 - - + -
1036H GLU* 3.7 7.0 - - + +
1039H ALA* 3.3 20.4 - - + -
1040H LEU* 3.1 34.1 - - + -
1043H TYR* 2.8 32.0 + - + -
701I LEU* 3.7 33.9 - - + -
702I LEU 2.8 19.3 - - - +
703I ASN* 3.3 28.7 - - + +
707I THR* 3.9 5.6 - - + -
710I ARG 3.6 2.7 + - - +
712I GLY* 1.3 77.2 - - - +
714I GLN* 1.3 63.7 + - - +
736I PHE* 3.7 0.2 - - - -
748I HIS* 5.8 3.6 - - + -
763I MET* 4.8 2.8 - - + +
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Residues in contact with GLN 714 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043H TYR* 3.8 7.0 - - - +
701I LEU* 3.3 3.4 - - - -
702I LEU 2.9 28.1 + - - -
711I LEU* 3.4 41.5 - - - +
713I ILE* 1.3 75.3 - - - +
715I ALA* 1.3 60.1 + - - +
716I PHE* 3.3 24.0 - - + -
732I VAL* 2.8 35.8 - - - +
735I ALA* 3.7 10.1 - - - +
736I PHE* 3.3 18.8 - - + -
763I MET* 3.9 6.7 - - - +
765I SER* 3.7 15.5 + - - +
768I ASN* 4.5 7.7 + - - +
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Residues in contact with ALA 715 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699I VAL* 4.1 14.1 - - + -
700I VAL 3.2 11.7 - - - +
701I LEU* 4.3 3.8 - - + +
714I GLN* 1.3 72.9 - - - +
716I PHE* 1.3 66.7 + - - +
759I ALA* 3.4 30.5 - - + +
763I MET* 3.2 12.3 + - + +
764I LEU* 3.3 15.7 - - + +
765I SER 3.0 21.5 + - - -
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Residues in contact with PHE 716 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639I LEU 3.4 14.4 - - - -
640I HIS 3.6 3.8 - - - -
641I GLN 3.0 22.2 - - - -
642I CYS* 3.2 26.2 - - + -
699I VAL* 3.0 8.3 - - - +
700I VAL* 2.9 32.5 + - - +
702I LEU* 4.2 22.7 - - + -
714I GLN* 3.3 50.5 - - + -
715I ALA* 1.3 76.5 - - - +
717I GLN* 1.3 61.1 + - - +
718I PRO* 3.2 3.9 - - - +
728I LEU* 4.4 8.3 - - + -
729I HIS* 4.7 2.0 - - + -
732I VAL* 4.1 21.3 - - + -
736I PHE* 4.4 5.6 - + - -
764I LEU* 5.0 0.4 - - - -
765I SER* 3.4 17.0 - - - -
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Residues in contact with GLN 717 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640I HIS* 3.2 46.2 + - + +
641I GLN* 3.5 9.9 - - + +
642I CYS 3.1 19.3 + - - -
695I ILE 5.2 0.2 - - - +
696I HIS 4.0 15.3 + - - +
697I GLY* 3.7 11.6 - - - +
698I LYS 3.9 8.5 - - - +
699I VAL* 3.9 9.1 - - + +
716I PHE* 1.3 70.8 - - - +
718I PRO* 1.3 75.2 - - - +
719I VAL* 3.4 5.3 + - + +
760I ARG* 3.0 27.7 + - - -
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Residues in contact with PRO 718 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642I CYS* 3.5 7.6 - - - +
644I LEU* 3.6 22.0 - - + -
692I GLU* 5.1 0.2 - - - +
695I ILE* 3.5 40.2 - - + +
696I HIS 5.7 0.2 - - - +
698I LYS 3.4 17.7 - - - +
699I VAL* 3.6 4.5 - - - -
700I VAL* 3.3 38.4 - - + -
716I PHE 3.2 8.5 - - - +
717I GLN* 1.3 89.7 - - - +
719I VAL* 1.3 61.7 + - - +
720I LEU* 3.9 1.9 + - - +
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Residues in contact with VAL 719 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G ASP 6.0 1.8 - - - +
637I LEU* 4.6 8.1 - - + -
641I GLN* 3.8 42.2 - - + +
642I CYS 3.3 8.6 + - - +
643I GLY* 4.0 1.9 - - - -
644I LEU 3.7 11.7 + - - -
692I GLU* 4.9 2.7 - - - +
717I GLN* 3.9 5.6 - - + +
718I PRO* 1.3 76.5 - - - +
720I LEU* 1.3 72.4 + - - +
721I VAL* 3.4 14.0 + - + +
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Residues in contact with LEU 720 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G THR* 3.5 19.3 - - + +
644I LEU* 3.4 7.6 - - + +
646I LYS* 4.0 22.7 - - + -
649I ALA* 4.6 4.9 - - + -
688I TRP* 5.1 4.3 - - + +
691I LEU* 3.9 33.4 - - + -
692I GLU* 2.9 45.1 + - + +
695I ILE* 3.7 39.3 - - + -
718I PRO* 4.1 2.9 - - + +
719I VAL* 1.3 75.4 - - - +
721I VAL* 1.3 67.5 + - - +
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Residues in contact with VAL 721 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G ASP* 5.6 7.9 - - + +
190G THR* 4.3 8.3 - - + -
636I GLN* 6.2 1.8 - - - +
643I GLY* 4.1 9.6 - - - -
644I LEU 3.0 32.5 + - - +
645I PRO* 3.5 7.6 - - + +
646I LYS* 3.2 28.1 + - - +
719I VAL* 3.4 13.0 - - + +
720I LEU* 1.3 82.4 - - - +
722I GLU* 1.3 70.5 + - - +
723I GLY 4.0 0.2 + - - -
725I SER 5.1 2.5 - - - +
727I GLN* 4.8 20.4 - - + +
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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