Contacts of the helix formed by residues 617 - 625 (chain A) in PDB entry 6FWF
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 PRO 617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A SER* 3.6 30.3 - - - +
236A SER* 5.3 1.1 - - - +
237A VAL* 6.1 0.9 - - + -
613A PHE* 3.1 27.1 - - + +
614A LEU 3.5 10.8 - - - +
615A ILE 3.5 1.0 - - - +
616A ASN* 1.3 93.7 - - + +
618A PRO* 1.4 62.3 - - + +
619A ILE* 3.9 15.5 - - + -
620A SER* 3.1 4.3 + - - +
621A LEU* 2.8 32.8 + - - +
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Residues in contact with PRO 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PRO* 4.1 2.2 - - - +
229A ASN* 3.2 44.0 - - + +
232A TRP* 6.1 2.0 - - + -
233A SER* 3.6 13.2 - - - +
544A TYR* 3.8 23.3 - - + +
545A PHE* 3.7 16.8 - - + -
553A MET* 5.2 4.0 - - + +
557A ALA* 5.4 7.4 - - + -
616A ASN 3.4 8.3 - - - +
617A PRO* 1.4 81.8 - - + +
619A ILE* 1.3 54.6 + - - +
621A LEU* 4.2 4.3 - - + -
622A PHE* 2.8 35.2 + - - +
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Residues in contact with ILE 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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225A PRO* 3.9 28.9 - - + +
229A ASN* 4.8 1.2 - - - +
230A TYR* 4.4 22.9 - - + -
233A SER* 3.8 16.1 + - - +
234A PHE* 5.4 9.0 - - + -
617A PRO* 3.1 18.9 - - + -
618A PRO* 1.3 77.7 - - - +
620A SER* 1.3 62.5 + - - +
622A PHE* 4.4 0.7 - - - +
623A TYR* 3.7 24.1 - - + -
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Residues in contact with SER 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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614A LEU* 3.8 25.9 + - - +
617A PRO* 3.1 7.4 + - - -
619A ILE* 1.3 81.8 - - - +
621A LEU* 1.3 63.1 + - - +
622A PHE 3.2 1.6 - - - -
623A TYR* 3.3 6.9 + - - +
624A ILE* 2.8 54.0 + - - +
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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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541A HIS 3.3 26.7 - - - +
542A HIS 5.2 0.2 - - - +
544A TYR* 3.6 22.9 - - + -
545A PHE* 3.7 8.9 - - + -
615A ILE* 3.2 41.8 + - + +
616A ASN 4.4 0.7 - - - +
617A PRO 2.8 17.2 + - - +
620A SER* 1.3 70.8 - - - +
622A PHE* 1.3 60.2 + - - +
624A ILE* 4.2 4.5 - - - -
625A GLN* 2.8 68.0 + - - +
1001A HEM 3.7 16.8 - - + -
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Residues in contact with PHE 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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213A ASN 3.7 6.5 - - - -
214A ASN* 3.1 41.7 - - + -
215A TRP* 2.7 35.6 + + - -
217A HIS* 3.5 33.1 + + + +
223A ASN 3.4 22.7 - - - -
224A VAL* 3.7 9.4 - - - -
225A PRO* 3.7 21.3 - - + -
545A PHE* 3.5 27.0 - + - -
618A PRO 2.8 24.7 + - - +
619A ILE 4.4 0.2 - - - +
621A LEU* 1.3 72.1 - - - +
623A TYR* 1.3 82.2 + + + +
703A LEU* 5.1 1.7 - - - +
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Residues in contact with TYR 623 (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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217A HIS* 3.3 46.1 + + + -
224A VAL* 3.3 17.7 - - + +
225A PRO* 4.7 6.3 - - + -
619A ILE* 3.7 24.5 - - + -
620A SER* 3.3 5.5 + - - +
622A PHE* 1.3 88.4 - + + +
624A ILE* 1.3 67.2 + - + +
625A GLN 3.3 1.4 + - - -
627A LEU* 3.5 8.5 - - + +
695A ALA* 4.9 2.0 - - + +
698A SER* 3.5 24.7 - - - +
699A ILE* 3.6 38.4 + - + +
703A LEU* 3.3 27.0 - - - +
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Residues in contact with ILE 624 (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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614A LEU* 5.1 8.5 - - + +
615A ILE* 3.4 46.0 - - + -
620A SER* 2.8 46.2 + - - +
621A LEU* 4.2 0.9 - - - -
623A TYR* 1.3 73.2 - - + +
625A GLN* 1.3 52.1 + - - +
626A GLY 2.7 19.1 + - - -
627A LEU* 2.8 24.6 + - + +
629A THR* 3.0 36.3 + - + +
630A SER* 3.7 5.0 + - - +
695A ALA* 4.8 9.2 - - + -
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Residues in contact with GLN 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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73A LEU 3.7 18.2 - - - +
74A GLY* 3.9 6.3 - - - +
75A HIS* 2.9 34.9 + - - -
215A TRP* 3.5 35.4 - - + +
542A HIS* 4.0 10.3 + - - +
545A PHE* 3.7 16.6 - - + +
621A LEU* 2.8 52.7 + - - +
623A TYR 3.3 5.1 - - - +
624A ILE* 1.3 68.6 - - - +
626A GLY* 1.3 60.7 + - - +
703A LEU* 4.3 5.4 - - - +
1001A HEM 3.2 18.1 + - - +
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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