Contacts of the strand formed by residues 6959 - 6969 (chain C) in PDB entry 6W75
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 LEU6959 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6921C LYS* 4.3 12.5 + - - +
6922C TRP 3.4 17.0 - - - +
6923C ASP 4.3 1.6 - - - -
6925C ILE* 3.9 21.3 - - + -
6954C PHE 3.5 1.0 + - - -
6955C ILE* 3.3 25.4 + - + +
6956C GLN 5.9 0.2 - - - -
6957C GLN 3.7 1.2 + - - -
6958C LYS* 1.3 78.6 - - - +
6960C ALA* 1.3 72.0 + - - +
6961C LEU* 3.7 0.9 + - - +
6963C GLY* 4.1 11.2 - - - +
6964C SER 4.0 14.4 - - - +
6965C VAL* 3.7 23.1 - - + -
6985C PHE* 3.7 9.4 - - + -
7009C TYR* 3.6 43.3 - - + -
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Residues in contact with ALA6960 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6921C LYS* 3.9 10.0 - - + +
6922C TRP 2.8 19.9 + - - +
6923C ASP* 3.8 15.9 - - - +
6959C LEU* 1.3 78.5 - - - +
6961C LEU* 1.3 64.8 - - - +
6962C GLY 3.4 0.2 + - - -
6963C GLY* 3.0 16.6 + - - -
7009C TYR* 3.7 3.0 - - - -
7079C ILE* 3.9 11.2 - - + -
7080C ILE 3.5 14.8 - - - +
7081C ARG* 3.9 17.5 - - + -
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Residues in contact with LEU6961 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6921C LYS* 5.6 0.2 - - - +
6959C LEU 3.7 1.4 + - - +
6960C ALA* 1.3 72.0 - - - +
6962C GLY* 1.3 58.5 - - - +
6963C GLY 3.5 1.2 + - - -
7009C TYR* 3.4 13.0 - - + +
7010C LEU* 3.5 8.7 - - - +
7011C GLY* 3.5 36.6 - - - +
7065C ILE* 3.8 41.1 - - + -
7073C LEU* 3.7 12.6 - - + -
7079C ILE* 3.3 6.6 - - - +
7080C ILE* 2.9 51.6 + - + +
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Residues in contact with GLY6962 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6858C ALA* 3.8 11.8 + - - +
6961C LEU* 1.3 69.9 - - - +
6963C GLY* 1.3 63.1 + - - +
6964C SER* 4.2 0.9 + - - -
7008C ASN* 3.1 26.4 + - - -
7009C TYR 2.8 21.0 + - - -
7073C LEU* 3.8 14.1 - - - +
7078C LEU 3.6 16.4 - - - -
7079C ILE* 3.7 5.8 - - - -
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Residues in contact with GLY6963 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6858C ALA* 5.6 0.2 - - - -
6923C ASP* 3.2 17.7 - - - -
6959C LEU* 4.1 10.5 - - - -
6960C ALA 3.0 17.5 + - - -
6961C LEU 3.2 1.4 + - - -
6962C GLY* 1.3 79.9 - - - +
6964C SER* 1.3 58.4 + - - -
6985C PHE* 3.8 0.3 - - - -
7008C ASN 3.3 3.3 + - - -
7009C TYR* 2.7 27.6 + - - +
7079C ILE* 3.8 7.3 - - - +
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Residues in contact with SER6964 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6852C LEU* 6.4 0.4 - - - -
6857C LEU* 3.3 34.0 - - - +
6858C ALA 5.2 0.3 + - - -
6923C ASP 3.1 7.9 + - - -
6924C LEU* 3.2 15.2 - - - -
6925C ILE 3.0 21.0 + - - -
6959C LEU* 4.0 1.6 - - - +
6962C GLY 4.2 0.7 + - - -
6963C GLY* 1.3 70.8 - - - -
6965C VAL* 1.3 69.1 + - - +
6985C PHE* 4.3 0.9 - - - -
7005C ILE* 5.9 1.6 - - - -
7006C GLY 3.2 11.7 - - - -
7007C CYS* 3.4 3.8 - - - -
7008C ASN* 3.1 24.3 + - - -
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Residues in contact with VAL6965 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6852C LEU* 6.0 0.4 - - - -
6924C LEU* 4.6 3.4 - - - -
6925C ILE* 3.1 27.1 - - + +
6955C ILE* 4.1 9.9 - - + -
6959C LEU* 3.7 24.7 - - + -
6964C SER* 1.3 81.3 - - - +
6966C ALA* 1.3 60.1 + - - +
6967C ILE* 4.1 18.2 - - + -
6982C MET* 4.0 15.7 - - + -
6985C PHE* 3.9 15.5 - - + -
7004C LEU 4.3 1.6 - - - +
7005C ILE* 3.2 10.0 - - - +
7006C GLY 2.9 41.9 + - - +
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Residues in contact with ALA6966 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6848C LEU* 4.2 22.2 - - + -
6852C LEU* 4.6 7.0 - - + -
6924C LEU* 5.9 0.2 - - + -
6925C ILE 2.9 6.7 + - - -
6926C ILE* 3.4 23.2 - - + +
6927C SER 2.9 25.8 + - - +
6965C VAL* 1.3 73.5 - - - +
6967C ILE* 1.3 61.3 + - - +
6968C LYS 4.2 0.4 - - - -
7003C PHE* 4.4 4.6 - - + -
7004C LEU 3.4 5.6 - - - -
7005C ILE* 4.1 17.0 - - + -
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Residues in contact with ILE6967 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6925C ILE* 4.1 17.3 - - + -
6927C SER* 3.7 28.5 - - - +
6947C PHE* 6.0 0.2 - - + -
6948C PHE* 4.1 9.0 - - + -
6951C ILE* 4.0 26.7 - - + -
6955C ILE* 4.8 1.1 - - + -
6965C VAL* 4.1 22.4 - - + -
6966C ALA* 1.3 80.0 - - - +
6968C LYS* 1.3 74.0 + - - +
6969C ILE* 3.5 1.4 + - - +
6978C LEU* 3.5 33.2 - - + -
7003C PHE* 4.1 1.8 - - - -
7004C LEU* 2.8 43.0 + - + +
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Residues in contact with LYS6968 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6844C LYS* 4.2 3.4 - - - +
6927C SER* 2.8 22.3 + - - +
6928C ASP* 2.7 40.3 + - - +
6929C MET 4.2 8.9 - - - +
6930C TYR* 3.7 34.5 - - + -
6947C PHE* 5.3 0.3 - - - -
6948C PHE* 3.9 13.0 - - - -
6967C ILE* 1.3 75.9 - - - +
6969C ILE* 1.3 79.3 + - - +
6970C THR* 4.1 4.5 - - + -
6973C SER* 5.0 1.1 + - - +
7001C GLU* 2.9 38.5 + - + +
7002C ALA 3.4 6.1 - - - +
7003C PHE* 3.6 13.6 - - + -
7105C SAM 4.4 8.3 - - - +
7108C FMT 3.9 9.9 + - - -
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Residues in contact with ILE6969 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6948C PHE* 4.2 14.8 - - + -
6967C ILE 4.0 2.5 - - - +
6968C LYS* 1.3 80.8 - - - +
6970C THR* 1.3 68.0 + - - +
6973C SER* 3.1 16.4 - - - +
6974C TRP* 4.4 6.5 - - + -
6975C ASN 5.4 0.4 - - - +
6978C LEU* 4.4 2.9 - - + -
6979C TYR* 3.1 31.2 - - + +
7001C GLU* 3.3 5.0 - - - -
7002C ALA* 2.8 44.0 + - + +
7004C LEU* 3.6 39.9 - - + -
7023C HIS* 4.3 10.5 - - + +
7026C TYR* 4.5 10.5 - - + -
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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