Contacts of the strand formed by residues 615 - 622 (chain A) in PDB entry 1FNS
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 615 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A LEU 3.1 6.7 + - - -
513A LEU* 3.5 7.5 - - - -
514A ASP 2.9 23.7 + - - -
614A ALA* 1.3 79.2 - - - +
616A ARG* 1.3 65.8 + - - +
617A ILE* 5.2 0.4 - - - -
647A ILE* 5.1 8.2 - - - +
697A LEU* 2.7 30.7 + - - -
698A ALA* 3.9 12.1 - - - -
699A PRO* 3.4 12.0 - - - +
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Residues in contact with ARG 616 (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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514A ASP* 3.5 14.6 + - + +
606A PHE* 3.6 36.6 - - + -
609A ILE* 3.4 41.8 - - - +
611A ARG 3.2 17.6 + - - -
612A PRO* 3.4 11.3 + - - +
614A ALA 3.2 24.9 + - - +
615A SER* 1.3 78.3 - - - +
617A ILE* 1.3 65.7 + - - +
644A LYS 3.8 2.9 + - - -
645A LYS* 3.0 48.6 + - - +
646A VAL* 3.6 13.4 - - - -
647A ILE* 2.8 27.9 + - - +
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Residues in contact with ILE 617 (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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513A LEU* 3.8 18.2 - - + -
514A ASP 2.9 8.3 + - - +
515A LEU* 3.7 18.7 - - + +
516A VAL* 2.8 35.1 + - - +
606A PHE* 5.2 0.6 - - - -
615A SER* 5.2 0.7 - - - -
616A ARG* 1.3 81.6 - - - +
618A ALA* 1.3 65.1 + - - +
619A LEU* 4.2 1.1 - - - +
646A VAL* 4.5 2.5 - - - -
647A ILE* 3.3 22.4 - - + +
649A ILE* 3.9 17.3 - - + -
694A LEU* 3.8 34.1 - - + +
697A LEU* 3.7 28.0 - - + -
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Residues in contact with ALA 618 (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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516A VAL* 3.8 7.9 - - + -
518A LEU* 4.3 17.0 - - + -
598A LEU* 5.0 3.8 - - + -
601A THR* 4.5 13.0 - - + -
617A ILE* 1.3 72.6 - - - +
619A LEU* 1.3 57.0 + - - +
620A LEU* 3.4 3.4 + - + -
641A LEU* 5.5 0.2 - - + -
646A VAL* 4.2 14.9 - - + +
647A ILE 2.8 13.5 + - - +
648A VAL* 3.6 16.5 - - + +
649A ILE 2.7 31.9 + - - -
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Residues in contact with LEU 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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515A LEU* 4.3 10.1 - - + -
516A VAL 2.9 15.5 + - - +
517A PHE* 3.8 32.9 - - + -
518A LEU* 3.0 25.2 + - - +
536A PHE* 4.3 15.0 - - + -
540A MET* 4.2 18.2 - - + -
617A ILE* 3.9 1.8 - - + -
618A ALA* 1.3 69.8 - - - +
620A LEU* 1.3 60.0 + - - +
621A LEU* 3.4 10.9 + - + +
649A ILE* 3.7 33.7 - - + +
651A VAL* 3.8 15.9 - - + -
690A ILE* 4.5 4.7 - - + -
694A LEU* 4.3 18.2 - - + -
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Residues in contact with LEU 620 (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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518A LEU* 4.0 13.9 - - + -
558A TYR* 3.5 33.4 - - + +
594A THR* 4.3 9.4 - - + -
597A VAL* 3.9 17.9 - - + -
598A LEU* 4.1 22.7 - - + -
618A ALA 3.4 4.4 + - - +
619A LEU* 1.3 69.5 - - - +
621A LEU* 1.3 59.1 + - - +
622A MET* 3.4 30.2 + - + +
634A PHE* 5.5 0.2 - - + -
648A VAL* 4.6 5.8 - - + -
649A ILE 2.9 13.1 + - - +
650A PRO* 3.5 4.2 - - + +
651A VAL* 2.8 25.2 + - - -
665A ILE* 3.9 21.3 - - + -
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Residues in contact with LEU 621 (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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517A PHE* 4.3 10.1 - - + -
518A LEU 2.9 14.7 + - - +
519A LEU* 3.5 27.8 - - + -
520A ASP* 3.2 20.2 + - - +
533A LEU* 4.0 28.0 - - + +
536A PHE* 4.1 19.5 - - + -
537A VAL* 4.6 0.2 - - + -
558A TYR* 3.2 11.8 + - - -
619A LEU* 4.1 26.2 - - + +
620A LEU* 1.3 70.0 - - - +
622A MET* 1.3 59.1 + - - +
651A VAL* 3.7 32.8 - - + -
653A ILE* 4.2 11.0 - - + -
683A LEU* 4.3 1.6 - - + -
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Residues in contact with MET 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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520A ASP* 4.1 0.4 - - - +
558A TYR* 3.7 11.2 - - - +
594A THR* 4.0 15.3 - - + -
620A LEU* 3.4 41.3 - - + +
621A LEU* 1.3 72.3 - - - +
623A ALA* 1.3 56.0 + - - +
624A SER 3.8 3.4 - - - +
650A PRO* 4.2 11.7 - - - -
651A VAL 2.9 11.3 + - - +
652A GLY* 3.5 3.5 - - - -
653A ILE* 2.7 35.9 + - - +
657A ALA* 3.6 3.5 - - + +
658A ASN* 3.6 44.0 - - + +
661A GLN* 4.2 7.9 - - + +
662A ILE* 3.8 21.1 - - + -
665A ILE* 4.9 3.8 - - - -
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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