Contacts of the strand formed by residues 69 - 74 (chain F) in PDB entry 3EGC
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 VAL 69 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E LEU* 4.5 5.8 - - + -
122E ARG* 3.4 30.7 - - - +
67F SER* 3.2 16.7 - - - +
68F ASN* 1.3 82.8 - - - +
70F VAL* 1.3 63.8 + - - +
99F SER* 3.3 11.7 - - - +
101F LEU* 3.8 36.3 - - + +
122F ARG 6.0 0.2 - - - +
123F ARG 5.2 0.7 - - - +
124F VAL* 3.4 9.6 - - + -
125F ASP* 2.5 38.7 + - - +
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Residues in contact with VAL 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F VAL* 1.3 79.1 - - - +
71F GLY* 1.3 72.2 + - - +
72F LEU* 4.7 0.7 - - - +
89F VAL* 5.3 0.2 - - + -
98F TYR* 4.0 13.0 - - + -
99F SER 2.8 11.7 + - - +
100F VAL* 3.6 5.5 - - + -
101F LEU* 3.0 27.2 + - - +
124F VAL* 4.0 3.4 - - - -
126F GLY 3.6 6.1 - - - +
128F ILE* 4.6 3.4 - - + -
308F MET* 3.7 29.2 - - + -
311F LEU* 3.4 36.3 - - + -
312F ILE* 5.8 0.2 - - + -
315F ILE* 3.9 19.5 - - + -
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Residues in contact with GLY 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F VAL* 1.3 77.6 - - - +
72F LEU* 1.3 59.0 + - - -
73F ILE 3.9 0.4 - - - -
101F LEU* 3.8 2.7 - - - -
119F PHE* 3.7 14.6 - - - -
124F VAL* 3.9 7.1 - - - +
126F GLY 3.0 12.1 + - - -
127F LEU* 3.3 21.1 - - - +
128F ILE 2.8 28.6 + - - +
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Residues in contact with LEU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LEU* 5.2 3.1 - - + -
70F VAL* 4.0 1.0 + - + -
71F GLY* 1.3 73.4 - - - -
73F ILE* 1.3 62.3 - - - +
74F VAL* 3.9 22.9 - - + -
85F VAL* 5.6 3.4 - - + -
86F ALA* 3.7 36.6 - - + +
89F VAL* 4.4 14.1 - - + -
100F VAL* 3.8 21.3 - - + -
101F LEU 2.8 15.1 + - - +
102F LEU* 3.5 11.8 - - + +
103F ALA 2.9 26.0 + - - +
119F PHE* 3.8 0.6 - - - -
128F ILE* 3.4 35.4 - - + +
130F ALA 5.7 0.4 - - - +
152F VAL* 5.8 1.3 - - + -
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Residues in contact with ILE 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F GLY 4.8 0.9 - - - -
72F LEU* 1.3 71.7 - - - +
74F VAL* 1.3 64.5 + - - +
103F ALA* 3.6 8.7 - - + +
105F THR* 3.7 25.8 - - + -
112F GLU* 4.3 5.8 - - + +
115F ALA* 3.7 7.9 - - + -
116F VAL* 3.7 43.1 - - + +
119F PHE* 3.6 31.2 - - + -
127F LEU* 4.3 11.9 - - + -
128F ILE 2.9 10.2 + - - +
129F LEU* 3.5 22.7 - - + +
130F ALA* 2.7 29.0 + - - +
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Residues in contact with VAL 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F LEU* 3.9 30.7 - - + -
73F ILE* 1.3 78.3 - - - +
75F SER* 1.3 62.0 + - - +
76F ASP 3.3 15.9 + - - +
77F ILE* 3.4 33.9 - - + +
82F PHE* 3.8 25.1 - - + +
85F VAL* 5.9 3.1 - - + -
86F ALA* 5.1 0.9 - - + +
102F LEU* 4.8 2.2 - - + -
103F ALA 3.0 11.0 + - - +
104F ASN* 3.6 2.8 - - - +
105F THR* 3.0 28.3 + - - +
130F ALA* 3.8 10.8 - - + -
152F VAL* 6.1 0.7 - - + -
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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