Contacts of the strand formed by residues 68 - 76 (chain A) in PDB entry 1CF5
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 ASN 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.3 2.4 - - - +
65A ASP* 2.9 35.3 + - - +
66A VAL 3.1 1.8 + - - -
67A THR* 1.3 88.2 - - - +
69A VAL* 1.3 62.0 + - - +
70A TYR* 2.8 60.2 + - + +
161A ARG* 3.1 14.4 + - - -
190A TRP* 3.6 4.6 - - - -
239A LEU* 3.9 20.6 - - + -
240A ASN* 4.3 3.8 - - - +
243A ALA* 5.8 0.9 - - + -
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Residues in contact with VAL 69 (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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21A PHE* 3.6 33.7 - - + -
25A LEU* 4.4 7.4 - - + -
37A LEU* 3.8 16.8 - - + -
64A ILE* 3.8 11.0 - - + +
65A ASP 2.9 9.6 + - - -
66A VAL 4.3 1.8 - - - -
68A ASN* 1.3 79.3 - - - +
70A TYR* 1.3 63.5 + - - +
71A VAL 3.7 0.2 + - - -
157A ALA* 3.6 26.5 - - + +
161A ARG* 3.4 15.2 + - - +
190A TRP* 4.1 7.4 - - + -
237A LEU* 3.7 31.2 - - + -
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Residues in contact with TYR 70 (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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64A ILE* 3.4 2.4 - - - -
65A ASP* 2.9 30.2 + - + +
68A ASN* 2.8 55.7 + - + +
69A VAL* 1.3 74.4 - - - +
71A VAL* 1.3 68.3 + - - +
72A VAL* 4.7 4.0 - - + -
107A GLY 6.2 0.7 - - - -
108A ASN* 6.5 1.6 - - + -
157A ALA* 5.7 0.2 - - - -
161A ARG* 4.0 21.5 - - - -
190A TRP* 4.5 7.5 - + - -
239A LEU* 5.5 4.9 - - - +
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Residues in contact with VAL 71 (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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62A VAL* 4.3 13.5 - - + -
63A ALA 3.3 10.3 - - - +
64A ILE* 4.0 17.0 - - + -
69A VAL 4.7 3.1 - - - +
70A TYR* 1.3 80.0 - - - +
72A VAL* 1.3 61.7 + - - +
73A ALA 4.4 7.2 - - - +
74A TYR* 6.0 1.1 - - + -
83A PHE* 3.5 34.4 - - + -
107A GLY* 5.4 2.6 - - - +
149A LEU* 5.0 3.8 - - + -
152A LEU* 5.0 8.1 - - + -
153A ILE* 3.9 37.5 - - + -
156A THR* 5.4 1.8 - - - +
157A ALA* 4.7 4.0 - - + -
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Residues in contact with VAL 72 (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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47A PHE* 3.7 28.3 - - + -
63A ALA* 2.9 29.7 + - + +
65A ASP* 3.7 28.0 - - + +
70A TYR* 4.0 5.6 - - + +
71A VAL* 1.3 77.6 - - - +
73A ALA* 1.3 65.0 + - - +
82A PHE* 4.8 0.2 - - - -
83A PHE* 3.1 33.6 + - - +
86A SER* 3.7 8.9 + - - +
87A PRO* 4.2 21.1 - - + -
90A ALA* 4.7 4.7 - - + -
94A LEU* 4.1 6.5 - - + -
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Residues in contact with ALA 73 (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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62A VAL* 3.8 2.0 - - - +
63A ALA* 2.8 33.1 + - + +
71A VAL* 3.7 5.8 - - - +
72A VAL* 1.3 87.8 - - + +
74A TYR* 1.3 60.4 + - - +
81A TYR 3.2 14.8 - - - +
82A PHE* 3.4 31.6 - - + -
83A PHE* 4.9 3.1 - - - +
95A PHE* 3.9 12.6 - - + -
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Residues in contact with TYR 74 (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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60A ILE* 4.5 12.6 - - + -
61A SER 3.5 9.6 - - - +
62A VAL* 4.0 15.5 - - + -
71A VAL* 6.0 1.8 - - + -
73A ALA* 1.3 77.6 - - - +
75A ARG* 1.3 66.9 + - - +
76A THR* 3.8 15.7 - - + -
80A SER* 3.4 0.2 - - - -
81A TYR* 2.8 60.8 + + + -
83A PHE* 6.5 0.2 - + - -
95A PHE* 3.9 6.1 - - - -
103A LEU* 4.7 7.9 - - + -
137A LEU* 2.7 54.9 + - + +
138A PHE 4.5 0.4 - - - -
140A TYR* 3.1 29.6 - + - +
145A ALA* 6.0 0.2 - - + -
149A LEU* 4.5 21.5 - - + -
152A LEU* 5.9 1.3 - - + -
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Residues in contact with ARG 75 (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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59A THR* 4.5 10.9 + - - +
60A ILE* 3.6 5.4 - - - -
61A SER* 2.8 50.7 + - - +
74A TYR* 1.3 76.5 - - - +
76A THR* 1.3 59.0 + - - +
77A ARG* 2.9 40.8 + - - +
79A VAL 3.3 14.6 - - - +
80A SER* 3.9 6.1 - - - -
95A PHE* 3.7 36.8 - - + +
98A THR* 3.6 23.6 - - + -
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Residues in contact with THR 76 (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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59A THR 5.0 0.9 - - - -
60A ILE* 4.8 5.2 - - - -
74A TYR* 3.8 9.4 - - + -
75A ARG* 1.3 72.0 - - - +
77A ARG* 1.3 98.8 + - - +
78A ASP 2.8 10.6 + - - -
79A VAL* 2.9 18.2 + - + +
81A TYR* 3.1 38.4 - - + +
137A LEU 3.9 2.0 - - - +
138A PHE* 2.7 29.3 + - - +
140A TYR* 5.0 0.2 - - + -
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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