Contacts of the strand formed by residues 603 - 612 (chain B) in PDB entry 1GGT
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 603 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B ASN* 3.4 26.3 + - - -
557B ILE* 4.2 2.6 - - - +
558B THR* 3.1 45.0 + - - +
559B PHE 4.1 4.2 + - - -
560B TYR* 4.4 1.7 + - - -
598B LEU* 4.9 0.9 - - - +
599B LEU* 5.7 0.8 + - - +
601B GLN* 3.4 5.4 - - - +
602B ALA* 1.3 79.2 - - - +
604B LEU* 1.3 70.0 + - - +
624B SER* 5.4 0.2 - - - -
625B THR 3.0 11.0 - - - -
626B VAL* 3.8 11.0 - - - -
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Residues in contact with LEU 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B PHE* 4.5 11.4 - - + -
556B ASN 3.3 7.0 - - - +
557B ILE* 3.5 33.2 - - + -
558B THR* 4.5 1.8 - - - -
568B PHE* 3.9 20.2 - - + -
594B TYR* 4.4 6.1 - - + -
598B LEU* 3.7 10.1 - - + -
603B SER* 1.3 79.1 - - - +
605B HIS* 1.3 60.3 + - - +
606B PHE* 3.7 20.2 - - + -
624B SER* 3.0 6.7 - - - -
625B THR* 2.8 42.8 + - - +
627B LEU* 4.0 35.4 - - + -
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Residues in contact with HIS 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B VAL* 5.7 5.3 - - + +
371B ASN* 5.6 0.4 - - - -
459B HIS* 5.6 0.8 + - - -
554B SER 3.9 0.3 - - - +
555B ALA* 3.3 2.9 - - - -
556B ASN* 2.7 36.0 + - + +
558B THR* 3.7 26.5 - - + +
604B LEU* 1.3 74.4 - - - +
606B PHE* 1.3 70.9 + - - +
607B PHE* 3.2 41.5 - + - -
622B GLN* 2.6 35.2 + - - +
623B LYS 3.2 12.3 + - - -
624B SER* 3.0 25.4 - - - +
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Residues in contact with PHE 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B PHE* 4.1 17.7 - + + -
524B VAL* 3.7 30.3 - - + -
533B PHE* 4.3 17.7 - + - -
535B LEU* 3.8 20.4 - - + -
553B LEU* 5.2 2.0 - - + -
554B SER 3.2 3.1 - - - +
555B ALA* 3.3 30.3 - - + -
568B PHE* 4.0 12.1 - + - -
589B ILE* 4.8 3.1 - - + -
604B LEU* 3.7 25.1 - - + -
605B HIS* 1.3 77.1 - - - +
607B PHE* 1.3 64.0 + - - +
608B VAL* 4.0 2.7 - - + -
622B GLN* 3.1 30.1 - - - +
623B LYS 2.9 17.5 + - - +
624B SER* 4.7 0.2 - - - -
625B THR* 3.5 23.8 - - + -
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Residues in contact with PHE 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B ILE* 4.2 24.5 - - + -
360B VAL* 3.7 42.2 - - + -
365B THR* 4.9 9.0 - - + -
441B TYR* 5.1 6.1 - + - -
552B TYR 3.4 5.4 - - - +
553B LEU* 3.5 1.4 - - - -
554B SER* 2.7 39.1 + - - +
556B ASN* 3.8 20.9 - - - -
564B PRO* 6.4 2.2 - - + -
605B HIS* 3.2 36.6 - + - -
606B PHE* 1.3 70.3 - - - +
608B VAL* 1.3 62.7 + - - +
609B THR* 3.8 4.1 + - + -
621B LYS 3.8 2.9 - - - -
622B GLN* 3.8 25.8 - - + -
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Residues in contact with VAL 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B MET* 3.3 33.5 - - + +
522B PHE* 3.5 43.1 - - + -
537B ILE* 4.4 20.6 - - + -
551B ALA* 5.4 3.1 - - + -
552B TYR 3.3 9.0 - - - +
553B LEU* 4.0 24.5 - - + -
606B PHE* 4.0 0.4 - - + -
607B PHE* 1.3 73.7 - - - +
609B THR* 1.3 59.7 + - - +
620B ALA* 3.4 2.3 - - - -
621B LYS 2.9 32.5 + - - -
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Residues in contact with THR 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU* 4.1 17.3 - - + -
358B GLY 3.0 22.0 + - - -
359B ASN* 4.3 2.9 - - - -
360B VAL* 4.0 25.1 - - + +
441B TYR* 5.1 3.1 - - + -
520B MET* 4.1 0.5 - - - +
551B ALA* 3.4 2.3 - - - +
552B TYR* 2.7 43.7 + - - +
607B PHE* 3.8 3.7 + - + -
608B VAL* 1.3 78.6 - - - +
610B ALA* 1.3 61.8 + - - +
618B VAL* 4.8 2.5 - - - -
619B LEU 3.1 6.1 - - - -
620B ALA* 3.7 22.0 - - + -
621B LYS 5.2 0.4 - - - +
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Residues in contact with ALA 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B GLY* 4.9 1.1 + - - -
520B MET* 3.5 20.9 - - + -
539B PHE* 4.7 2.2 - - + -
549B ILE* 3.9 12.1 - - + -
550B THR 3.4 8.3 - - - -
551B ALA* 3.7 14.8 - - + -
552B TYR* 4.6 3.3 - - - -
609B THR* 1.3 80.7 - - - +
611B ARG* 1.3 62.9 + - - +
612B ILE 4.3 0.2 - - - -
618B VAL* 3.0 12.3 - - - +
619B LEU* 2.7 34.9 + - + +
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Residues in contact with ARG 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B ASP* 3.3 29.4 + - - +
358B GLY* 5.5 1.1 - - - -
549B ILE* 3.2 4.4 - - - -
550B THR* 3.0 51.5 + - - +
552B TYR* 2.9 32.7 + - + -
610B ALA* 1.3 76.9 - - - +
612B ILE* 1.3 69.9 + - - +
613B ASN* 2.9 39.8 + - - +
616B ARG* 4.6 16.6 - - + +
617B ASP 3.8 2.9 - - - -
618B VAL* 4.6 8.1 - - + +
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Residues in contact with ILE 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515B ARG 3.9 2.9 - - - +
516B SER* 3.0 28.7 - - - +
518B VAL* 3.5 34.3 - - + -
547B TYR* 3.8 17.7 - - + -
548B THR 3.7 3.4 - - - -
549B ILE* 3.7 17.5 - - + -
611B ARG* 1.3 69.7 - - - +
613B ASN* 1.3 57.7 + - - +
614B GLU* 3.0 20.9 + - - +
615B THR* 4.0 8.1 - - - +
616B ARG* 2.7 34.4 + - - -
617B ASP* 3.1 24.0 + - + +
619B LEU* 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
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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