Contacts of the strand formed by residues 139 - 147 (chain G) in PDB entry 6PSS
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 139 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71G LYS* 3.7 15.4 + - - -
72G GLU 5.6 0.9 - - - +
103G ASN* 5.7 0.3 - - - +
104G LYS 2.5 29.7 + - - -
105G SER* 3.5 14.4 - - - -
133G LEU* 4.6 1.6 - - - -
137G ASN 4.0 2.6 + - - -
138G ALA* 1.3 77.0 - - - +
140G ILE* 1.3 71.1 + - - +
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Residues in contact with ILE 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G ILE* 5.4 2.5 - - + -
71G LYS* 3.9 27.8 - - + +
74G VAL* 5.5 4.0 - - + -
102G LEU* 3.7 36.6 - - + +
103G ASN* 3.7 13.2 - - - +
104G LYS* 3.2 13.4 + - + +
110G VAL* 4.3 7.0 - - + -
131G CYS* 4.1 17.5 - - - -
133G LEU* 3.7 20.9 - - + -
139G SER* 1.3 88.0 + - - +
141G SER* 1.3 70.7 + - - +
142G MET* 3.9 18.6 - - + -
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Residues in contact with SER 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G ILE* 3.3 5.4 - - - +
62G ASP* 3.1 49.8 + - - +
71G LYS* 4.8 3.6 - - - +
101G THR* 6.2 0.2 - - - -
102G LEU 3.4 4.9 - - - -
103G ASN* 3.4 14.7 + - - -
140G ILE* 1.3 82.8 + - - +
142G MET* 1.3 63.2 + - - +
143G ARG* 5.4 3.1 - - - -
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Residues in contact with MET 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G VAL* 4.6 1.8 - - + -
60G GLU 3.2 7.9 - - - +
61G ILE* 3.9 20.0 - - + -
81G ILE* 3.7 29.2 - - + -
85G LEU* 3.8 23.3 - - - -
101G THR* 3.3 24.8 - - - +
102G LEU* 3.0 53.4 + - + +
130G ILE* 3.8 10.3 - - + -
131G CYS* 4.8 4.0 - - - -
140G ILE* 3.9 17.0 - - + -
141G SER* 1.3 76.4 - - - +
143G ARG* 1.3 68.5 + - - +
144G ILE* 4.0 10.5 - - + -
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Residues in contact with ARG 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G GLU 3.5 3.3 - - - +
59G VAL* 4.5 0.4 - - - -
60G GLU* 2.7 60.4 + - + +
62G ASP* 2.3 40.0 + - - +
99G ILE* 3.7 24.7 - - + +
100G LEU 3.3 7.6 - - - +
101G THR* 4.5 13.9 - - + +
141G SER* 4.8 4.0 + - - -
142G MET* 1.3 83.1 + - - +
144G ILE* 1.3 59.7 + - - +
145G LYS* 3.3 7.7 + - - +
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Residues in contact with ILE 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G VAL* 3.8 26.5 - - + -
58G GLU 3.8 2.2 - - - -
59G VAL* 4.2 9.6 - - + -
85G LEU* 3.8 26.7 - - + -
88G LEU* 4.6 4.5 - - + -
98G VAL 3.6 0.2 - - - +
99G ILE* 4.3 0.2 - - - -
100G LEU* 2.8 40.0 + - + +
102G LEU* 3.7 32.1 - - + +
115G ILE* 4.1 30.3 - - + -
142G MET* 4.0 20.4 - - + -
143G ARG* 1.3 70.2 - - - +
145G LYS* 1.3 58.9 + - - +
146G VAL* 3.1 9.1 + - + +
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Residues in contact with LYS 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G VAL* 3.6 2.2 - - - -
57G THR* 2.8 45.0 + - - +
58G GLU* 2.7 55.7 + - + +
97G GLU* 3.3 28.3 + - + +
98G VAL 3.8 3.1 - - - -
99G ILE* 3.7 35.7 - - + +
143G ARG 3.3 2.7 + - - +
144G ILE* 1.3 68.8 - - - +
146G VAL* 1.3 71.4 + - - +
147G GLN* 3.4 11.1 + - - +
158G ARG* 6.4 0.2 - - - +
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Residues in contact with VAL 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G CYS* 3.2 40.2 - - + +
55G ALA 4.4 0.4 - - - +
56G VAL* 4.0 16.8 - - + +
90G VAL* 3.9 17.0 - - + -
92G VAL* 4.0 12.1 - - + -
97G GLU* 3.3 4.7 - - - +
98G VAL* 3.0 39.5 + - + +
100G LEU* 3.7 30.5 - - + -
144G ILE* 3.1 4.7 + - + +
145G LYS* 1.3 76.9 - - - +
147G GLN* 1.3 63.8 + - - +
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Residues in contact with GLN 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G CYS* 3.6 7.1 - - - -
55G ALA 3.2 16.8 + - - +
57G THR* 3.6 24.9 + - + +
96G ASP 3.4 7.2 - - - +
97G GLU* 3.0 28.8 - - + +
145G LYS* 3.4 14.1 + - + -
146G VAL* 1.3 80.1 - - - +
148G ARG* 1.3 70.6 + - - +
158G ARG* 5.7 4.0 - - - +
177G TYR* 3.2 27.4 + - - +
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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