Contacts of the strand formed by residues 621 - 629 (chain B) in PDB entry 5FLM
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 ILE 621 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B TYR* 5.0 9.6 - - + +
391B LYS 5.5 3.6 + - - +
393B LEU* 4.1 24.0 - - + -
485B LEU* 5.0 0.7 - - + -
508B MET* 3.2 58.4 - - + +
509B VAL* 4.3 7.0 - - + -
526B LEU* 3.7 21.8 - - + -
530B ALA* 4.1 12.8 - - + -
531B TYR 4.0 5.2 - - - +
532B ILE* 4.3 9.2 - - + +
619B GLY 3.3 2.6 + - - +
620B ARG* 1.3 70.5 - - - +
622B CYS* 1.3 62.3 + - - +
666B ASP* 3.5 10.9 - - - +
667B THR* 3.9 12.2 + - + +
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Residues in contact with CYS 622 (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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508B MET* 4.0 2.7 - - - -
530B ALA* 4.9 0.7 - - - -
531B TYR* 2.7 61.7 + - - +
533B SER* 4.3 13.7 - - - -
600B GLU* 5.2 7.0 - - - -
620B ARG* 4.1 14.6 - - - +
621B ILE* 1.3 75.7 - - - +
623B ARG* 1.3 61.0 + - - +
664B TYR* 4.5 16.9 - - + -
665B ILE 3.3 25.4 - - - +
666B ASP* 3.6 9.6 - - + +
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Residues in contact with ARG 623 (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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506B TRP* 3.4 25.9 + - - -
507B GLY* 3.7 27.6 - - - +
508B MET* 3.9 14.8 - - + -
529B MET* 3.9 17.9 - - + +
530B ALA* 4.5 3.1 - - - -
622B CYS* 1.3 75.4 - - - +
624B PRO* 1.3 74.6 + - + +
625B LEU* 3.2 29.9 - - + +
664B TYR* 4.3 3.1 - - - -
665B ILE* 2.9 33.4 + - - +
670B GLU* 3.2 19.4 + - - +
675B LEU* 3.4 18.8 - - - +
697B GLU* 3.3 30.2 + - - +
703B ILE* 5.6 1.8 - - - +
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Residues in contact with PRO 624 (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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33B TYR* 4.4 6.3 - - + -
529B MET* 3.3 47.6 - - + +
531B TYR* 5.6 0.2 - - + -
622B CYS 4.7 0.4 - - - +
623B ARG* 1.3 92.7 + - + +
625B LEU* 1.3 71.5 + - - +
653B TRP* 3.9 28.0 - - + -
662B VAL* 5.1 0.9 - - + -
663B GLU 3.3 13.0 - - - +
664B TYR* 4.1 19.7 - - + -
698B ILE* 4.4 9.7 - - + +
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Residues in contact with LEU 625 (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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623B ARG* 3.2 39.7 - - + +
624B PRO* 1.3 79.7 - - - +
626B LEU* 1.3 63.2 + - - +
662B VAL* 3.4 4.4 - - - -
663B GLU* 2.9 32.5 + - - +
665B ILE* 3.7 33.4 - - + -
670B GLU* 5.2 2.9 - - + +
673B VAL* 5.4 1.1 - - + -
675B LEU* 3.5 24.5 - - + -
695B HIS* 4.0 13.0 - - + -
696B CYS 4.3 1.3 - - - +
697B GLU* 3.8 29.2 - - + -
698B ILE* 4.5 8.3 - - - +
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Residues in contact with LEU 626 (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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22B TRP* 3.3 38.1 - - + -
29B VAL* 5.8 2.2 - - + -
625B LEU* 1.3 72.6 - - - +
627B ILE* 1.3 61.0 + - - +
633B LEU* 4.4 18.6 - - + -
635B LEU* 3.9 29.8 - - + +
661B VAL* 3.9 5.2 - - + -
662B VAL* 3.7 22.7 - - + -
695B HIS* 2.9 30.5 - - - +
696B CYS* 3.1 25.2 + - + +
697B GLU 4.4 4.5 - - - +
698B ILE* 3.5 20.3 - - + +
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Residues in contact with ILE 627 (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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592B ARG* 3.4 42.4 - - + +
625B LEU 4.3 0.2 - - - +
626B LEU* 1.3 79.3 - - - +
628B VAL* 1.3 64.3 + - - +
629B GLU* 3.7 6.3 - - - +
633B LEU* 3.8 5.0 - - - +
634B LEU* 3.1 40.7 + - + +
635B LEU 4.9 0.2 + - - -
660B GLY 3.2 24.5 - - - +
661B VAL 3.2 17.3 + - - +
662B VAL 4.1 0.9 - - - +
663B GLU* 3.3 41.5 - - + +
694B THR 3.8 4.9 - - - +
695B HIS* 4.1 2.7 - - - +
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Residues in contact with VAL 628 (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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627B ILE* 1.3 77.4 - - - +
629B GLU* 1.3 69.4 + - - +
630B LYS 3.2 23.5 + - - +
631B GLN 4.0 2.0 - - - -
632B LYS 3.6 11.4 - - - +
633B LEU* 3.6 23.1 - - + -
683B GLN* 3.4 32.1 - - - +
693B TYR 3.3 16.5 - - - +
694B THR* 3.0 21.6 + - - +
695B HIS 3.7 21.3 - - - +
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Residues in contact with GLU 629 (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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588B ARG* 5.6 0.5 + - - -
592B ARG* 3.0 29.6 + - - -
627B ILE* 3.7 9.3 + - - +
628B VAL* 1.3 73.4 - - - +
630B LYS* 1.3 73.9 + - + +
632B LYS* 2.9 28.2 + - - +
634B LEU* 3.6 34.3 - - + +
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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