Contacts of the strand formed by residues 618 - 632 (chain A) in PDB entry 6CIM
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 LYS 618 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A GLY* 3.1 39.0 - - - +
604A ASP* 4.1 4.0 - - - +
605A VAL* 4.5 0.4 - - - -
616A PRO* 5.1 10.8 - - + -
617A GLU* 1.3 82.1 - - - +
619A ALA* 1.3 63.6 + - - +
659A LEU* 3.6 10.2 - - - +
660A ALA* 3.2 29.6 + - - +
661A ASP* 3.8 30.4 + - + +
662A GLU 5.4 0.7 - - - +
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Residues in contact with ALA 619 (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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601A GLY* 3.1 5.7 - - - -
602A MET* 2.7 45.2 + - + +
603A GLY 3.6 6.1 + - - -
605A VAL* 3.7 21.1 - - + +
618A LYS* 1.3 76.6 - - - +
620A VAL* 1.3 64.3 + - - +
657A LEU* 6.5 0.2 - - + -
658A MET 3.3 13.2 - - - +
659A LEU* 3.9 10.1 - - + -
660A ALA 3.7 1.5 - - - +
662A GLU 5.4 0.5 + - - -
968A PHE* 4.8 7.0 - - + -
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Residues in contact with VAL 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A CYS* 3.6 28.0 - - - -
600A ASP 3.4 9.0 - - - +
602A MET* 5.0 0.2 - - - -
619A ALA* 1.3 77.9 - - - +
621A ARG* 1.3 62.3 + - - +
622A PHE 4.2 0.2 - - - -
656A CYS 3.8 1.0 - - - +
657A LEU* 3.8 4.3 - - - +
658A MET* 2.9 66.7 + - + +
660A ALA* 3.1 23.3 - - + +
661A ASP 4.2 0.9 - - - +
662A GLU* 3.8 26.0 - - + +
668A LEU* 4.2 8.5 - - + -
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Residues in contact with ARG 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A SER* 3.9 13.5 - - - -
599A CYS* 3.2 8.9 - - - +
600A ASP* 3.0 58.4 + - - +
602A MET* 3.5 37.7 - - + +
620A VAL* 1.3 75.0 - - - +
622A PHE* 1.3 59.8 + - - +
623A SER* 3.1 43.4 + - - +
652A CYS* 3.8 11.2 - - - -
654A PRO* 5.3 3.4 - - + -
656A CYS 3.7 3.8 - - - -
657A LEU* 3.9 13.2 - - + -
961A ASN* 3.0 40.0 + - - +
964A GLY* 5.7 3.6 - - - -
991A HIS* 5.2 9.6 - - - -
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Residues in contact with PHE 622 (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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559A TYR* 4.3 16.8 - + - -
597A GLU* 4.0 25.8 - - + -
598A SER 3.6 11.4 - - - -
599A CYS* 3.7 13.5 - - + -
620A VAL 4.2 0.4 - - - -
621A ARG* 1.3 71.5 - - - +
623A SER* 1.3 57.3 + - - +
654A PRO* 4.2 0.3 - - - +
655A LEU* 2.8 40.4 + - + +
656A CYS* 2.9 31.5 + - + +
658A MET* 5.1 1.8 - - + -
672A LEU* 3.8 32.8 - - + -
675A LEU* 3.4 29.4 - - + -
676A ILE* 4.1 14.4 - - + -
707A TYR* 3.5 20.0 - - - -
785A ILE* 4.6 2.5 - - + -
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Residues in contact with SER 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A GLU* 3.7 5.0 - - - +
598A SER* 2.9 33.3 + - - +
621A ARG* 3.1 44.1 + - - +
622A PHE* 1.3 74.7 + - - +
624A PHE* 1.3 65.8 + - - +
652A CYS* 3.4 20.4 + - - -
653A LYS 3.4 12.3 + - - -
654A PRO* 3.8 5.7 - - - +
655A LEU* 4.2 2.7 - - - +
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Residues in contact with PHE 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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559A TYR* 4.0 12.6 - + + +
562A ALA* 3.7 44.6 - - + -
563A LEU* 3.9 20.6 - - + -
566A ALA* 4.0 16.4 - - + -
595A VAL* 3.7 24.0 - - + -
596A LYS 3.2 11.4 - - - +
597A GLU* 4.7 0.2 - - + -
598A SER* 5.2 0.4 - - - -
623A SER* 1.3 76.5 - - - +
625A THR* 1.3 68.1 + - - +
626A VAL* 4.3 10.3 - - + -
651A CYS 3.9 0.2 - - - +
653A LYS* 3.1 43.9 + - + +
655A LEU* 3.5 25.8 - - + -
992A TRP* 4.2 8.7 - + - -
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Residues in contact with THR 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL* 4.5 0.7 - - - -
596A LYS* 2.8 53.9 + - - -
598A SER* 4.5 4.0 + - - -
624A PHE* 1.3 79.2 + - - +
626A VAL* 1.3 73.5 + - - +
627A MET* 3.1 14.9 + - - +
643A GLU* 4.7 1.8 - - + -
646A PRO 3.9 19.9 + - - +
651A CYS* 3.5 32.1 + - + +
652A CYS* 3.8 14.4 - - - +
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Residues in contact with VAL 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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563A LEU* 4.9 3.1 - - + -
566A ALA* 4.6 10.8 - - + -
567A LEU* 5.2 3.8 - - + -
570A MET* 3.8 27.7 - - + +
593A VAL* 4.0 26.5 - - + -
594A VAL 4.0 3.8 - - - -
595A VAL* 4.6 6.1 - - + +
624A PHE* 4.2 22.0 - - + -
625A THR* 1.3 70.9 - - - +
627A MET* 1.3 61.7 + - - +
628A ARG 4.5 1.3 - - - +
629A ILE* 4.0 9.4 - - + -
641A PHE* 3.7 22.8 - - + -
643A GLU* 3.6 19.4 - - - +
651A CYS* 4.8 1.6 + - - +
653A LYS* 5.8 2.5 - - + +
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Residues in contact with MET 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A VAL* 2.8 27.5 + - + +
595A VAL 4.7 0.2 - - - -
596A LYS* 3.5 26.0 - - + +
625A THR* 3.4 27.1 - - - +
626A VAL* 1.3 72.4 - - - +
628A ARG* 1.3 72.7 + - + +
641A PHE* 4.6 0.7 - - - -
642A GLU* 3.6 5.5 - - - +
643A GLU* 3.1 26.5 + - + +
646A PRO* 3.9 31.9 - - + -
955A ALA* 4.9 5.6 - - + +
956A TRP* 4.1 34.5 - - + -
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Residues in contact with ARG 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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592A THR 3.7 0.9 - - - +
593A VAL* 3.6 3.3 - - - +
594A VAL* 2.9 57.6 + - + +
626A VAL 3.7 0.2 - - - -
627A MET* 1.3 90.7 + - + +
629A ILE* 1.3 64.5 - - - +
630A THR* 4.6 11.9 - - + -
639A LYS* 3.7 23.4 - - + +
641A PHE* 3.1 17.9 - - - +
642A GLU* 3.0 27.7 + - + +
703A ARG* 6.1 1.8 - - - +
950A ASP 4.3 16.4 + - - -
956A TRP* 4.5 16.3 - - - -
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Residues in contact with ILE 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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567A LEU* 3.9 18.8 - - + -
570A MET* 4.0 12.3 - - - -
574A ILE* 3.6 33.9 - - + -
591A PHE* 4.0 29.8 - - + -
592A THR 3.1 15.3 - - - +
593A VAL* 4.3 7.6 - - + -
626A VAL* 4.0 7.4 - - + -
628A ARG* 1.3 79.2 - - - +
630A THR* 1.3 64.4 + - - +
640A VAL* 3.0 13.0 + - + +
641A PHE* 2.9 47.8 + - + +
698A PHE* 5.0 2.0 - - + -
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Residues in contact with THR 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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591A PHE* 3.2 10.8 - - - +
592A THR* 2.9 49.2 + - - +
594A VAL* 5.9 2.0 - - + +
628A ARG* 4.2 15.2 - - + -
629A ILE* 1.3 79.7 - - - +
631A ILE* 1.3 60.3 + - - +
637A ASN* 4.4 23.7 + - + +
638A VAL 3.1 14.4 - - - +
639A LYS* 3.8 20.6 - - + +
640A VAL* 4.3 1.3 - - - +
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Residues in contact with ILE 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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578A MET* 4.5 5.8 - - - -
583A LEU* 3.5 26.5 - - + -
587A LEU* 3.9 31.9 - - + -
589A GLY* 3.7 21.3 - - - +
590A PRO 3.9 2.2 - - - -
591A PHE* 3.6 32.8 - - + -
630A THR* 1.3 75.8 - - - +
632A GLU* 1.3 70.1 + - - +
633A HIS* 3.3 4.2 + - + -
637A ASN* 3.5 3.8 - - - -
638A VAL* 2.8 36.5 + - + +
640A VAL* 3.7 13.9 - - + -
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Residues in contact with GLU 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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587A LEU* 6.0 0.2 - - - +
589A GLY* 5.2 3.1 - - - -
590A PRO* 3.6 35.3 + - + +
631A ILE* 1.3 77.5 - - - +
633A HIS* 1.3 60.8 + - - +
634A GLY 3.5 22.2 + - - +
635A SER* 5.4 2.1 - - - -
636A GLN 3.3 9.4 - - - +
637A ASN* 3.8 13.2 + - - +
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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