Contacts of the strand formed by residues 61 - 71 (chain C) in PDB entry 3STJ
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 PHE 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C VAL* 3.8 24.5 - - + -
32C GLU* 3.4 6.9 - - - +
33C GLY* 3.2 34.9 + - - +
34C THR 3.3 44.6 - - - -
59C GLN 4.6 1.3 - - - +
60C PRO* 1.3 75.4 - - - +
62C GLU* 1.3 67.2 + - - +
63C GLY* 3.9 12.8 - - - -
86C GLN* 3.7 46.7 - - + -
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Residues in contact with GLU 62 (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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30C ARG* 3.1 33.4 + - + +
31C VAL 3.3 3.1 - - - +
32C GLU* 3.1 37.3 - - + +
61C PHE* 1.3 77.2 - - - +
63C GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 63 (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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30C ARG* 3.6 6.4 - - - +
31C VAL* 2.8 40.3 + - - +
61C PHE* 3.9 15.0 - - - -
62C GLU* 1.3 73.4 - - - +
64C LEU* 1.3 63.0 + - - +
83C VAL* 5.9 2.2 - - - -
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Residues in contact with LEU 64 (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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28C SER* 3.8 17.5 - - - +
29C VAL 3.5 9.4 - - - +
30C ARG* 4.4 19.5 - - + +
63C GLY* 1.3 73.9 - - - +
65C GLY* 1.3 76.6 + - - +
83C VAL* 4.8 3.5 - - - +
146C ASN* 3.9 27.1 - - + +
149C GLY* 4.2 18.8 - - - +
185C GLY* 4.0 13.2 + - - -
187C SER* 5.6 0.5 + - - -
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Residues in contact with GLY 65 (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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28C SER* 3.7 2.1 - - - -
29C VAL* 2.8 33.9 + - - +
64C LEU* 1.3 82.8 - - - +
66C SER* 1.3 60.3 + - - -
83C VAL* 3.9 19.5 - - - +
146C ASN* 4.2 1.1 - - - +
185C GLY* 3.7 12.3 - - - -
187C SER* 4.0 6.3 - - - -
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Residues in contact with SER 66 (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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26C VAL* 5.0 0.9 - - - -
27C VAL 3.3 12.3 - - - -
28C SER* 4.4 0.2 - - - +
29C VAL* 3.6 7.7 - - - +
65C GLY* 1.3 74.8 - - - -
67C GLY* 1.3 59.5 + - - +
79C THR* 2.9 22.3 + - - -
144C VAL 4.8 0.2 - - - -
145C GLY* 3.4 11.0 - - - -
146C ASN* 2.9 18.8 + - - +
185C GLY 2.8 19.2 + - - -
186C ASN 3.5 2.5 + - - -
187C SER 3.0 7.1 + - - -
188C GLY* 3.3 9.0 - - - +
189C GLY* 3.6 22.2 - - - -
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Residues in contact with GLY 67 (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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26C VAL* 3.3 11.3 - - - +
27C VAL* 2.7 43.4 + - - +
29C VAL* 3.7 3.7 - - - +
66C SER* 1.3 74.8 - - - +
68C VAL* 1.3 63.5 + - - -
77C VAL* 3.9 4.9 - - - -
78C LEU 3.4 7.2 - - - -
79C THR* 4.4 0.4 - - - -
188C GLY 3.3 8.7 - - - -
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Residues in contact with VAL 68 (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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25C ALA 3.6 6.5 - - - +
26C VAL* 4.6 1.1 - - + -
67C GLY* 1.3 78.1 - - - +
69C ILE* 1.4 64.4 + - - +
70C ILE* 3.3 3.3 + - + +
77C VAL* 3.2 5.8 - - - +
78C LEU* 2.8 38.9 + - + +
127C ILE* 3.6 42.2 - - + -
188C GLY 4.1 0.2 - - - +
189C GLY 3.9 1.6 - - - -
190C ALA* 3.6 36.1 - - + +
198C LEU* 4.2 8.5 - - + -
201C ILE* 3.7 24.7 - - + -
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Residues in contact with ILE 69 (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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24C PRO 4.2 8.3 - - - +
25C ALA 2.8 16.9 + - - +
27C VAL* 3.6 27.4 - - + -
68C VAL* 1.4 68.2 - - - +
70C ILE* 1.3 60.6 + - - +
71C ASN 3.8 6.3 - - - +
72C ALA* 3.8 28.9 - - - +
76C TYR 3.5 7.2 - - - +
77C VAL* 3.9 15.0 - - + -
94C LEU* 4.2 7.4 - - + -
118C ILE* 4.5 2.5 - - + -
124C LEU* 3.8 26.0 - - + -
125C THR 3.3 27.1 - - - +
126C GLN* 3.4 1.2 - - - -
127C ILE* 2.9 32.7 + - - +
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Residues in contact with ILE 70 (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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68C VAL* 3.3 6.2 + - + +
69C ILE* 1.3 73.2 - - - +
71C ASN* 1.4 62.5 + - + +
76C TYR* 2.8 32.1 + - + +
78C LEU* 3.6 34.8 - - + +
115C LEU* 4.3 10.3 - - + -
126C GLN* 3.9 16.4 - - - +
127C ILE* 4.4 12.0 - - + +
129C ILE* 3.7 34.2 - - + +
198C LEU* 5.2 2.7 - - + -
225C ARG* 4.8 6.3 - - + -
228C ALA* 4.2 14.6 - - + -
232C ILE* 6.1 1.1 - - + -
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Residues in contact with ASN 71 (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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69C ILE* 3.8 3.4 - - - +
70C ILE* 1.4 78.2 - - + +
72C ALA* 1.4 53.2 + - - +
73C SER* 3.1 14.4 + - - -
74C LYS* 3.0 40.4 + - - +
75C GLY* 2.8 31.2 + - - -
76C TYR* 3.0 36.1 + - + -
126C GLN* 3.4 8.5 + - - +
232C ILE* 6.1 1.2 - - - +
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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