Contacts of the helix formed by residues 634 - 652 (chain F) in PDB entry 4MNE
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 SER 634 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573F ILE* 3.5 25.0 - - - +
601F LYS* 5.5 4.7 - - - +
623F GLU* 5.0 0.2 + - - -
632F PRO 4.7 0.2 + - - -
633F TYR* 1.3 77.9 - - - +
635F PHE* 1.3 66.1 + - - +
636F GLN* 3.2 26.1 + - - +
637F SER* 2.8 27.6 + - - -
638F ASP 3.2 5.4 + - - -
701F ARG* 4.0 19.4 + - - +
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Residues in contact with PHE 635 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D ASN 5.7 2.0 - - - -
320D GLU* 4.1 13.7 - - - -
568F HIS* 3.3 71.8 - + + +
571F SER* 4.4 7.6 - - - -
572F ILE 4.3 2.0 - - - -
573F ILE* 4.1 15.5 - - + -
601F LYS* 3.8 41.5 - - + +
634F SER* 1.3 73.1 - - - +
636F GLN* 1.3 63.3 + - - +
638F ASP* 3.0 8.3 + - - +
639F VAL* 2.9 26.3 + - - +
706F LEU* 3.7 26.9 - - + -
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Residues in contact with GLN 636 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671C ARG* 5.1 10.5 - - - +
634F SER* 3.4 15.3 + - - +
635F PHE* 1.3 85.1 + - - +
637F SER* 1.3 56.3 + - - +
639F VAL* 3.0 13.2 + - - +
640F TYR 2.9 22.3 + - - -
701F ARG* 3.2 31.7 + - + +
702F ASP* 5.3 6.2 + - - +
704F ARG* 3.1 35.3 + - + +
706F LEU* 3.5 31.2 - - + +
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Residues in contact with SER 637 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573F ILE* 4.8 1.6 - - - +
619F TRP 5.0 1.0 - - - +
621F ALA* 4.3 6.0 + - - +
623F GLU* 3.8 14.6 - - - -
624F VAL* 3.8 20.6 - - - -
632F PRO 4.5 0.7 - - - -
633F TYR* 3.4 14.2 - - - +
634F SER* 2.8 36.9 + - - -
636F GLN* 1.3 74.5 - - - +
638F ASP* 1.3 65.8 + - - +
640F TYR* 3.1 12.3 + - - +
641F ALA* 3.1 13.2 + - - +
704F ARG* 3.7 8.4 - - - +
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Residues in contact with ASP 638 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564F MET* 3.6 16.9 - - + +
568F HIS* 3.0 27.5 + - + +
573F ILE* 3.2 14.8 - - - +
574F HIS* 2.9 24.6 + - - +
575F ARG* 3.1 25.5 + - - -
576F ASP 4.8 0.3 + - - -
577F LEU* 4.1 8.5 + - - +
634F SER 3.2 5.0 + - - +
635F PHE 3.0 11.3 + - - +
637F SER* 1.3 76.9 + - - +
639F VAL* 1.3 57.8 + - - +
641F ALA* 3.3 7.9 + - - +
642F PHE* 2.9 28.1 + - - +
707F PHE* 4.3 1.8 - - - -
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Residues in contact with VAL 639 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635F PHE 2.9 19.6 + - - +
636F GLN* 3.0 12.5 + - - +
638F ASP* 1.3 77.5 - - - +
640F TYR* 1.3 55.2 + - - +
642F PHE* 3.3 5.0 - - - +
643F GLY 2.8 23.0 + - - -
696F CYS* 3.6 29.1 - - + +
704F ARG* 4.1 7.0 - - + -
705F PRO 3.3 28.3 - - - +
706F LEU* 4.2 7.6 - - + -
707F PHE* 3.5 30.3 - - + -
710F ILE* 3.7 11.9 - - + -
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Residues in contact with TYR 640 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618F LEU 4.7 1.5 + - - -
619F TRP 3.5 12.1 - - - -
620F MET 3.3 20.9 + - - -
621F ALA* 3.4 22.7 - - + -
622F PRO* 3.8 18.8 - - + +
636F GLN 2.9 6.8 + - - +
637F SER 3.1 8.9 + - - +
639F VAL* 1.3 73.8 - - - +
641F ALA* 1.3 60.1 + - - +
643F GLY* 2.8 17.2 + - - -
644F ILE* 3.0 29.3 + - + +
656F TYR* 3.6 19.9 + - - -
669F VAL* 4.5 5.4 - - - +
675F SER* 5.6 0.9 - - - -
676F PRO* 4.4 4.9 - - + +
696F CYS 3.3 10.3 + - - -
697F LEU* 3.4 48.6 - - + +
704F ARG* 3.9 20.2 - - - -
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Residues in contact with ALA 641 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575F ARG 6.5 0.2 - - - -
577F LEU* 3.3 37.5 - - + +
619F TRP* 3.5 24.7 - - + +
637F SER 3.1 10.7 + - - +
638F ASP* 3.6 11.0 - - - +
640F TYR* 1.3 75.0 - - - +
642F PHE* 1.3 58.7 + - - +
644F ILE* 2.9 21.4 + - - +
645F VAL* 3.0 14.8 + - - +
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Residues in contact with PHE 642 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557F ALA* 3.6 28.5 - - + -
560F THR* 4.1 20.2 - - + -
561F ALA* 3.8 21.1 - - + -
577F LEU* 3.7 10.8 - - + +
638F ASP 2.9 13.4 + - - +
639F VAL 3.3 7.9 - - - +
641F ALA* 1.3 76.0 - - - +
643F GLY* 1.3 57.8 + - - +
645F VAL* 3.1 12.0 + - + +
646F LEU* 2.8 61.4 + - + +
692F LEU* 4.7 0.2 - - + -
696F CYS* 3.9 15.3 - - - -
707F PHE* 3.5 26.7 - + + -
710F ILE* 3.9 20.2 - - + -
714F ILE* 4.9 2.2 - - + -
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Residues in contact with GLY 643 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639F VAL 2.8 16.6 + - - -
640F TYR 2.8 8.5 + - - -
642F PHE* 1.3 72.7 - - - +
644F ILE* 1.3 56.6 + - - +
646F LEU* 3.3 10.6 - - - +
647F TYR* 3.0 22.0 + - - +
693F MET* 3.8 10.0 - - - +
696F CYS* 3.7 19.3 - - - -
697F LEU* 3.7 13.2 - - - +
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Residues in contact with ILE 644 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618F LEU 3.6 25.1 - - - +
619F TRP* 3.3 31.2 - - + +
640F TYR* 3.0 29.4 + - + +
641F ALA 2.9 9.3 + - - +
643F GLY* 1.3 73.8 - - - +
645F VAL* 1.3 62.2 + - - +
647F TYR* 3.0 8.7 + - + +
648F GLU* 2.8 28.1 + - - +
655F PRO* 4.1 24.5 - - + -
656F TYR* 5.0 1.1 - - - +
676F PRO* 3.8 22.9 - - + -
697F LEU* 3.6 20.0 - - + -
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Residues in contact with VAL 645 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537F LEU* 3.9 19.5 - - + -
557F ALA* 6.2 0.4 - - - -
560F THR* 5.3 6.5 - - + +
577F LEU* 4.7 4.3 - - + -
578F LYS* 4.4 3.6 - - - -
579F SER* 4.3 7.2 - - - +
582F ILE* 3.9 31.9 - - + -
619F TRP* 4.1 8.5 - - + +
641F ALA 3.0 13.3 + - - +
642F PHE* 3.3 17.3 - - + +
644F ILE* 1.3 76.7 - - - +
646F LEU* 1.3 63.6 + - - +
648F GLU* 3.1 19.1 + - + +
649F LEU* 2.9 32.4 + - + +
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Residues in contact with LEU 646 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557F ALA* 3.6 23.3 - - + -
642F PHE* 2.8 46.5 + - + +
643F GLY* 3.3 10.3 - - - +
644F ILE 3.2 0.2 - - - -
645F VAL* 1.3 72.6 - - - +
647F TYR* 1.3 57.6 + - - +
649F LEU* 3.5 6.9 + - + +
650F MET* 2.9 36.5 + - + +
689F MET* 3.6 26.5 - - + -
692F LEU* 3.7 21.1 - - + +
693F MET* 3.6 35.9 - - + +
696F CYS* 4.4 1.8 - - - -
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Residues in contact with TYR 647 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643F GLY 3.0 13.0 + - - +
644F ILE* 3.0 16.0 + - + +
646F LEU* 1.3 73.4 - - - +
648F GLU* 1.3 65.9 + - - +
650F MET 3.2 0.2 + - - -
651F THR* 2.8 58.9 + - + +
653F GLN* 3.5 21.0 + - + -
654F LEU 4.0 2.8 + - - -
655F PRO* 3.8 31.2 - - + +
656F TYR 5.1 1.6 + - - -
676F PRO* 3.7 24.5 - - + -
677F ASP* 3.3 34.8 + - - +
678F LEU* 4.0 12.8 - - + -
680F LYS* 3.5 16.3 + - - +
693F MET* 3.4 16.3 - - + -
697F LEU* 5.1 1.1 - - + -
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Residues in contact with GLU 648 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541F LEU* 3.8 14.3 - - + +
542F HIS* 3.0 24.6 + - - +
579F SER* 2.4 36.6 + - - -
619F TRP* 2.9 34.2 + - - -
644F ILE* 2.8 20.7 + - + +
645F VAL* 3.1 14.7 + - + +
647F TYR* 1.3 71.5 - - - +
649F LEU* 1.3 57.3 + - - +
652F GLY* 2.7 36.2 + - - -
653F GLN 3.5 18.8 - - - +
654F LEU* 3.7 9.3 - - + +
655F PRO* 5.1 0.9 - - + -
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Residues in contact with LEU 649 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537F LEU* 3.7 31.4 - - + -
541F LEU* 3.7 13.4 - - + +
553F LEU* 3.6 27.7 - - + +
556F ILE* 4.1 11.0 - - + -
557F ALA* 3.8 38.4 - - + +
560F THR* 5.8 0.2 - - - +
645F VAL* 2.9 31.5 + - + +
646F LEU* 3.6 10.5 - - + +
648F GLU* 1.3 72.8 - - - +
650F MET* 1.3 66.0 + - + +
682F ARG* 2.4 35.9 + - - +
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Residues in contact with MET 650 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550F MET* 3.9 18.2 - - - +
553F LEU* 3.7 39.0 - - + +
554F ILE* 4.9 1.6 - - + +
646F LEU* 2.9 25.3 + - + +
647F TYR 4.2 1.3 - - - +
649F LEU* 1.3 84.6 - - + +
651F THR* 1.3 58.2 + - - +
681F VAL* 3.5 12.8 - - + +
682F ARG* 2.9 35.1 + - - +
685F CYS* 3.7 33.9 - - - +
689F MET* 4.3 29.6 - - + +
693F MET* 4.6 7.6 - - + -
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Residues in contact with THR 651 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647F TYR* 2.8 53.6 + - + +
650F MET* 1.3 81.5 - - - +
652F GLY* 1.3 61.0 + - - +
653F GLN* 2.9 37.8 + - - +
680F LYS* 3.2 35.1 - - - +
681F VAL* 3.9 7.6 - - + +
682F ARG* 3.9 15.3 + - - +
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Residues in contact with GLY 652 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541F LEU* 4.0 12.8 - - - +
542F HIS* 3.5 20.2 + - - -
648F GLU 2.7 17.4 + - - -
651F THR* 1.3 73.1 - - - +
653F GLN* 1.3 60.4 + - - +
682F ARG* 3.4 24.7 - - - -
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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
------------------------------------------------------------
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