Contacts of the helix formed by residues 637 - 654 (chain D) in PDB entry 6UZA
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 PHE 637 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623C LEU* 4.0 25.8 - - + -
626C SER* 5.2 3.6 - - - -
627C LEU* 5.7 2.2 - - + -
633D ASP* 3.1 26.5 - - + -
634D ILE 3.2 6.3 + - - +
636D LYS* 1.3 87.1 - - + +
638D MET* 1.3 60.9 + - - +
639D VAL 3.1 2.6 + - - -
640D ILE* 3.4 14.3 + - + +
641D PHE* 3.0 26.8 + - + +
718D VAL* 5.1 9.7 - - + +
721D ASN* 3.9 25.1 - - - -
722D MET* 3.9 43.5 - - + -
725D ALA* 3.8 27.6 - - + -
726D MET* 5.0 3.6 - - + -
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Residues in contact with MET 638 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A VAL* 5.0 15.5 - - + -
717A ILE* 5.1 1.8 - - + -
1005A SBJ 5.6 10.3 - - + -
634D ILE* 3.0 45.0 + - + +
635D PHE* 4.0 31.9 - - + +
636D LYS 3.5 0.6 - - - -
637D PHE* 1.3 77.2 - - - +
639D VAL* 1.3 56.3 + - + +
641D PHE* 3.7 11.9 - - + -
642D ILE* 2.9 39.0 + - + +
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Residues in contact with VAL 639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C PHE* 3.7 43.1 - - + -
635D PHE 3.9 15.0 - - - +
636D LYS* 4.0 1.8 - - - +
637D PHE 3.1 1.0 - - - -
638D MET* 1.3 73.9 - - + +
640D ILE* 1.3 60.8 + - + +
642D ILE* 3.2 16.2 - - + +
643D MET* 3.0 52.5 + - + +
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Residues in contact with ILE 640 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614C LEU* 4.8 17.0 - - + -
620C PHE* 5.1 4.9 - - + -
623C LEU* 4.2 29.2 - - + -
624C GLN 5.0 0.2 - - - +
627C LEU* 4.0 32.5 - - + -
1003C S9Y 4.8 19.3 - - + +
636D LYS 4.9 6.3 - - - +
637D PHE* 3.4 13.6 + - + +
639D VAL* 1.3 73.9 - - + +
641D PHE* 1.3 65.2 + - - +
643D MET* 3.3 19.1 + - + +
644D VAL* 3.1 34.6 + - + +
718D VAL* 4.9 9.6 - - + -
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Residues in contact with PHE 641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637D PHE* 3.0 17.5 + - + +
638D MET* 3.5 14.8 - - + +
640D ILE* 1.3 78.4 - - - +
642D ILE* 1.3 64.5 + - + +
644D VAL* 3.4 0.8 + - - -
645D PHE* 2.9 35.6 + + + +
682D ILE* 3.7 40.4 - - + -
715D MET* 3.5 35.4 - - + +
718D VAL* 4.0 21.0 - - + +
719D LEU* 3.6 30.5 - - + -
722D MET* 6.4 0.9 - - - -
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Residues in contact with ILE 642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638D MET* 2.9 24.5 + - + +
639D VAL* 3.2 21.8 - - + +
641D PHE* 1.3 79.8 - - + +
643D MET* 1.3 62.2 + - + +
645D PHE* 3.9 9.9 - - + -
646D VAL* 2.9 39.5 + - + +
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Residues in contact with MET 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607C PHE* 4.6 5.6 - - + -
610C ILE* 3.7 39.0 - - + -
614C LEU* 4.0 30.5 - - + -
620C PHE* 5.9 1.1 - - + -
1003C S9Y 4.6 21.3 - - + +
1005C Y01 4.8 12.3 - - + -
639D VAL* 3.0 42.8 + - + +
640D ILE* 3.3 16.1 + - + +
642D ILE* 1.3 78.3 - - + +
644D VAL* 1.3 63.0 + - - +
646D VAL* 4.0 3.2 - - - +
647D ALA* 3.0 25.3 + - - +
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Residues in contact with VAL 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003C S9Y 3.8 30.5 - - + -
640D ILE* 3.1 23.7 + - + +
641D PHE* 5.0 0.2 - - - -
643D MET* 1.3 75.6 - - - +
645D PHE* 1.3 61.7 + - - +
647D ALA* 3.4 0.9 + - - +
648D PHE* 3.1 54.2 + - + +
711D TYR* 4.9 1.3 - - + -
714D THR* 3.8 25.8 - - + -
715D MET* 3.7 22.9 - - + -
718D VAL* 4.9 8.5 - - + -
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Residues in contact with PHE 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641D PHE* 2.9 28.6 + + + +
642D ILE* 3.8 11.4 - - + +
644D VAL* 1.3 77.8 - - - +
646D VAL* 1.3 60.3 + - + +
648D PHE* 3.5 0.5 + - - -
649D MET* 2.9 42.6 + - + +
675D PHE* 3.4 37.2 - + - -
678D LEU* 3.3 32.5 - - + +
679D PHE* 3.4 33.9 - + + -
682D ILE* 4.3 6.7 - - + -
711D TYR* 3.4 16.2 - + - -
715D MET* 3.9 10.5 - - + +
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Residues in contact with VAL 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607C PHE* 4.1 15.9 - - + -
1005C Y01 4.2 11.9 - - + -
642D ILE* 2.9 28.9 + - + +
643D MET* 4.0 3.6 - - - +
645D PHE* 1.3 76.3 - - + +
647D ALA* 1.3 64.7 - - - +
649D MET* 4.2 18.4 - - + -
650D ILE* 3.0 45.7 + - + +
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Residues in contact with ALA 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603C VAL* 5.0 0.5 - - - +
604C VAL* 3.9 16.4 - - - +
607C PHE* 3.7 39.5 - - + -
1003C S9Y 4.6 9.4 - - + -
643D MET 3.0 19.0 + - - +
644D VAL* 3.5 8.3 - - - +
646D VAL* 1.3 76.8 - - - +
648D PHE* 1.3 60.8 + - + +
650D ILE* 4.1 1.2 - - - +
651D GLY* 3.0 25.6 + - - -
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Residues in contact with PHE 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C VAL* 3.8 30.7 - - + -
1003C S9Y 4.0 19.7 - - + -
644D VAL* 3.1 43.5 + - + +
647D ALA* 1.3 78.4 - - + +
649D MET* 1.3 60.2 + - - +
652D MET* 3.0 40.5 + - + +
678D LEU* 3.7 17.5 - - + +
707D LEU* 3.6 33.7 - - + -
710D VAL* 3.7 26.2 - - + -
711D TYR* 3.8 26.2 - + + -
714D THR* 4.5 3.8 - - - -
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Residues in contact with MET 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645D PHE* 2.9 25.8 + - + +
646D VAL* 3.7 23.6 - - + +
648D PHE* 1.3 77.3 - - - +
650D ILE* 1.3 71.3 + - + +
653D PHE* 3.0 28.6 + - + +
671D VAL* 4.3 20.9 - - + +
674D SER* 3.1 33.2 + - - +
675D PHE* 3.7 37.2 - - + +
678D LEU* 3.5 9.8 - - + +
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Residues in contact with ILE 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C LEU 4.4 12.6 - - - +
458C VAL* 3.7 34.3 - - + -
603C VAL* 3.8 18.6 - - + -
607C PHE* 4.3 10.3 - - + -
1005C Y01 4.8 0.2 - - + -
646D VAL* 3.0 39.9 + - + +
647D ALA 4.2 1.8 - - - +
649D MET* 1.3 88.2 - - + +
651D GLY* 1.3 58.7 + - - +
653D PHE* 3.9 9.5 - - + +
654D ASN* 3.0 41.8 + - - +
671D VAL* 6.5 0.9 - - + -
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Residues in contact with GLY 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600C ALA* 3.3 28.4 - - - +
603C VAL* 3.8 14.3 - - - +
604C VAL* 3.7 26.0 - - - -
647D ALA 3.0 11.1 + - - -
649D MET 3.3 0.2 - - - -
650D ILE* 1.3 78.9 - - - +
652D MET* 1.3 60.7 + - - +
654D ASN* 3.8 1.5 + - - +
655D LEU 3.5 6.1 + - - -
707D LEU* 4.4 1.0 - - - +
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Residues in contact with MET 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C VAL* 5.8 0.2 - - + -
648D PHE* 3.0 23.9 + - + +
649D MET 4.4 0.9 - - - +
651D GLY* 1.3 74.3 - - - +
653D PHE* 1.3 61.6 + - - +
654D ASN 3.3 0.4 - - - -
655D LEU* 3.2 7.3 + - + +
656D TYR* 3.0 36.1 + - + +
668D PHE* 3.8 37.9 - - + +
678D LEU* 3.8 28.9 - - + -
691D VAL* 5.3 0.2 - - - -
704D GLY* 4.3 11.4 - - - +
707D LEU* 3.9 32.8 - - + +
708D TYR* 3.9 33.2 - - + +
711D TYR* 4.6 4.9 - - + -
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Residues in contact with PHE 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C ALA* 3.6 22.7 - - + -
464C ARG* 3.2 39.3 - - + -
465C PHE* 4.0 15.9 - + - -
649D MET* 3.0 20.2 + - + +
650D ILE* 3.9 9.6 - - + +
652D MET* 1.3 78.1 - - - +
654D ASN* 1.3 77.4 + - - +
657D SER* 3.2 33.3 + - - -
668D PHE 3.9 6.7 - - - -
669D THR 3.5 27.4 - - - -
670D THR 4.2 2.9 - - - -
671D VAL* 4.0 20.2 - - + -
674D SER* 4.1 12.6 + - - +
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Residues in contact with ASN 654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C LEU 4.3 9.6 + - - +
460C ASN* 6.2 0.2 - - - +
461C ALA* 3.6 19.6 - - - +
464C ARG* 4.3 15.1 + - - +
596C GLU* 4.7 9.5 - - - +
599C TYR* 3.5 36.8 + - + -
600C ALA* 5.0 4.9 - - - -
603C VAL* 3.9 16.8 - - - +
650D ILE* 3.0 25.9 + - - +
651D GLY* 4.0 6.3 - - - +
652D MET 3.3 0.2 - - - -
653D PHE* 1.3 92.1 - - - +
655D LEU* 1.3 59.8 + - - +
657D SER* 4.5 2.5 + - - -
658D TYR* 5.2 5.5 - - - -
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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