Contacts of the strand formed by residues 624 - 631 (chain A) in PDB entry 4C48
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 THR 624 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576A VAL 3.4 7.8 + - - -
577A GLN* 3.5 19.9 + - - -
587A THR* 4.1 5.4 - - - -
613A ASN* 3.7 4.3 - - - +
614A GLY* 2.8 27.2 + - - -
616A GLY* 3.2 38.9 - - - +
619A GLY 3.7 5.1 + - - +
620A ARG 4.0 0.2 - - - -
621A GLY* 3.5 30.5 - - - +
622A GLN 3.1 3.2 + - - -
623A ASN* 1.3 83.1 - - - +
625A GLY* 1.3 61.9 + - - +
626A ILE* 5.2 0.5 - - - +
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Residues in contact with GLY 625 (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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576A VAL* 2.8 39.8 + - - +
587A THR* 4.3 0.4 - - - +
591A LEU* 3.9 14.1 - - - -
612A VAL 3.2 13.5 - - - -
613A ASN* 4.4 0.2 - - - -
614A GLY 4.3 0.4 - - - -
615A PHE 4.8 1.3 - - - -
624A THR* 1.3 77.4 + - - +
626A ILE* 1.3 72.6 + - - +
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Residues in contact with ILE 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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573A MET* 4.5 8.3 - - + -
574A THR 3.3 15.9 - - - +
575A MET* 3.9 4.5 - - + -
576A VAL* 4.0 4.4 - - - +
591A LEU* 4.4 2.3 - - - +
610A PHE 4.1 0.5 - - - +
611A ALA* 3.2 1.6 - - - -
612A VAL* 2.7 42.8 + - + +
615A PHE* 3.2 27.1 - - + +
616A GLY* 4.2 6.1 - - - -
617A PHE* 3.4 39.5 - - + +
624A THR* 5.5 0.2 - - - +
625A GLY* 1.3 90.6 - - - +
627A ALA* 1.3 61.4 + - - +
628A PHE* 3.3 33.7 + - + -
666A PHE* 6.2 0.2 - - + -
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Residues in contact with ALA 627 (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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573A MET* 3.6 3.8 - - - -
574A THR* 2.9 47.4 + - + -
576A VAL* 5.0 3.1 - - + +
591A LEU* 5.9 1.3 - - + -
594A VAL* 4.8 12.3 - - + -
595A THR* 5.5 0.4 - - - +
598A TYR* 5.8 0.2 - - + -
609A VAL* 3.9 15.0 - - + -
610A PHE 3.3 4.5 - - - -
611A ALA* 3.7 17.0 - - + +
626A ILE* 1.3 74.2 - - - +
628A PHE* 1.3 64.8 + - - +
629A VAL* 3.6 5.2 - - + +
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Residues in contact with PHE 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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136A PHE* 4.2 18.2 - + - -
139A VAL* 3.6 35.2 - - + -
178A PHE* 3.8 27.4 - + - -
326A PRO 4.9 2.3 - - - +
327A TYR* 4.2 23.8 - + + -
572A PHE 4.0 4.3 - - - -
573A MET* 3.3 23.6 - - + -
608A SER 3.8 1.0 - - - +
609A VAL* 3.7 0.9 - - - -
610A PHE* 2.5 62.0 + + + +
612A VAL* 5.5 3.1 - - + -
615A PHE* 4.5 7.4 - + - -
626A ILE* 3.3 26.7 - - + -
627A ALA* 1.3 74.4 - - - +
629A VAL* 1.3 60.4 + - - +
630A SER 4.0 0.6 + - - -
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Residues in contact with VAL 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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326A PRO 4.3 2.7 - - - -
327A TYR* 5.0 0.9 - - - -
571A VAL* 3.3 7.6 - - - +
572A PHE* 3.0 60.8 + - + +
574A THR* 4.1 5.8 - - - +
598A TYR* 3.2 43.5 - - + -
606A VAL* 3.9 13.2 - - + -
608A SER 3.7 2.7 - - - +
609A VAL* 4.6 2.7 - - + +
627A ALA* 3.6 16.8 - - + +
628A PHE* 1.3 75.5 - - - +
630A SER* 1.3 73.2 + - - +
631A LEU* 4.4 0.4 - - + -
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Residues in contact with SER 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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325A TYR 5.2 1.9 + - - -
326A PRO* 3.2 25.2 + - - -
570A GLY 4.5 1.7 + - - -
571A VAL* 4.3 9.5 - - - +
606A VAL* 3.6 0.9 - - - -
607A GLU* 3.0 24.4 + - - +
608A SER* 2.9 30.9 + - - -
629A VAL* 1.3 87.8 - - - +
631A LEU* 1.3 71.1 + - - +
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Residues in contact with LEU 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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570A GLY 3.2 24.9 + - - +
572A PHE* 4.0 30.3 - - + -
605A ASN 3.4 4.7 - - - +
606A VAL* 3.8 24.9 - - + +
607A GLU* 3.4 8.9 - - - +
630A SER* 1.3 93.1 + - - +
632A LYS* 1.3 71.1 + - - +
633A ASP* 3.9 0.7 + - - -
637A ARG* 3.5 28.5 - - - +
644A VAL* 3.5 23.3 - - + -
647A ILE* 4.2 18.4 - - + -
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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