Contacts of the helix formed by residues 78 - 89 (chain A) in PDB entry 4FDI
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 LEU 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ASN* 3.2 22.6 + - - +
77A PRO* 1.3 79.4 - - - +
79A DDZ 1.3 65.8 + - - +
81A PRO* 3.8 9.3 - - + +
82A SER* 3.0 25.8 + - - -
106A ASN* 3.7 35.2 - - + +
107A ALA 3.5 35.7 - - - +
108A TYR* 4.0 9.0 - - + -
289A ASN* 3.2 13.4 - - - +
310A LYS* 4.5 1.3 - - - -
311A GLN* 4.0 15.9 - - - +
604A CIT 3.4 23.8 - - + +
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Residues in contact with DDZ 79 (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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39A ASP* 3.6 2.4 + - - -
78A LEU* 1.3 75.8 - - - +
80A SER* 1.3 67.6 + - - -
82A SER* 3.1 6.1 + - - -
83A ARG* 2.8 45.4 + - - +
140A LYS* 3.2 5.5 + - - -
142A HIS* 2.8 28.1 + - - -
288A ASP* 3.4 9.4 - - - -
289A ASN* 3.3 0.4 + - - -
603A CA 2.4 25.5 - - - -
604A CIT 2.6 24.9 + - - -
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Residues in contact with SER 80 (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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79A DDZ 1.3 74.6 + - - -
81A PRO* 1.4 72.3 - - - +
83A ARG* 3.2 4.3 + - - +
84A ALA* 2.9 24.4 + - - +
97A PHE* 3.7 12.7 - - - -
108A TYR* 3.4 6.5 - - - +
109A THR* 2.8 39.7 + - - -
142A HIS* 3.0 34.9 + - - +
143A LEU* 4.4 0.2 - - - +
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Residues in contact with PRO 81 (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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76A ASN* 3.4 27.4 - - - +
78A LEU* 3.8 10.8 - - + +
79A DDZ 3.5 3.8 - - - -
80A SER* 1.4 93.9 - - - +
82A SER* 1.3 56.1 + - - +
84A ALA* 3.4 2.9 + - - +
85A ALA* 2.9 28.6 + - - +
92A PRO* 3.6 16.9 - - + +
97A PHE* 3.5 34.8 - - + +
107A ALA 3.4 25.4 - - - +
108A TYR* 4.5 0.2 - - - -
486A LEU* 4.8 1.1 - - + -
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 3.1 14.0 + - - -
75A ALA* 4.5 3.8 - - - -
76A ASN* 3.2 18.6 + - - +
78A LEU 3.0 15.5 + - - -
79A DDZ 3.1 3.9 + - - -
81A PRO* 1.3 76.1 - - - +
83A ARG* 1.3 61.8 + - - +
85A ALA* 3.3 8.0 + - - +
86A LEU* 3.0 27.2 + - - +
288A ASP* 3.0 33.0 + - - -
342A ILE* 4.0 7.6 - - - +
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Residues in contact with ARG 83 (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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37A LEU* 3.8 16.8 - - + +
38A MET 3.9 4.9 + - - -
39A ASP* 3.3 33.5 + - - +
79A DDZ 2.8 34.6 + - - +
80A SER 3.7 5.6 - - - +
82A SER* 1.3 74.8 - - - +
84A ALA* 1.3 63.4 + - - +
86A LEU* 3.4 5.7 + - - +
87A LEU* 3.2 29.3 + - - +
140A LYS* 3.5 30.1 + - - +
141A TRP 3.9 13.7 - - - +
142A HIS* 3.9 8.1 - - - -
143A LEU* 3.8 15.9 - - + -
229A TYR* 3.8 14.9 + - - +
231A ALA* 3.5 19.6 + - - +
232A VAL 4.5 3.2 + - - -
288A ASP* 3.1 24.5 + - + +
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Residues in contact with ALA 84 (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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80A SER 2.9 16.3 + - - +
81A PRO 3.6 4.7 - - - +
83A ARG* 1.3 76.3 - - - +
85A ALA* 1.3 54.4 + - - +
87A LEU 3.5 0.7 + - - +
88A THR* 2.6 38.5 + - - +
95A ASN* 3.6 11.4 - - - +
97A PHE* 3.7 33.9 - - + -
117A ILE* 4.7 2.5 - - + -
143A LEU* 3.7 18.1 - - + +
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Residues in contact with ALA 85 (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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75A ALA* 3.4 31.4 - - + -
81A PRO 2.9 17.3 + - - +
82A SER 3.5 4.0 - - - +
83A ARG 3.2 0.2 - - - -
84A ALA* 1.3 74.9 - - - +
86A LEU* 1.3 57.9 + - - +
89A GLY* 2.9 30.8 + - - -
90A ARG 3.2 22.4 + - - +
92A PRO* 4.2 4.3 - - + -
95A ASN* 3.7 0.8 - - - +
342A ILE* 4.6 0.4 - - + -
343A MET* 3.5 10.4 - - + +
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Residues in contact with LEU 86 (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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35A LEU* 4.0 25.8 - - + -
37A LEU* 3.8 26.9 - - + -
82A SER 3.0 12.9 + - - +
83A ARG* 3.6 9.9 - - - +
85A ALA* 1.3 77.7 - - - +
87A LEU* 1.3 78.7 + - + +
124A LEU* 5.1 4.3 - - + +
229A TYR* 4.2 9.9 - - + +
342A ILE* 3.6 46.5 - - + +
345A LEU* 4.2 14.8 - - + -
346A PHE* 3.4 25.6 + - - +
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Residues in contact with LEU 87 (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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83A ARG 3.2 19.0 + - - +
84A ALA 3.5 2.4 + - - +
85A ALA 3.3 0.2 - - - -
86A LEU* 1.3 92.0 - - + +
88A THR* 1.3 59.5 + - - +
123A LEU* 3.2 20.9 - - + -
124A LEU* 2.9 32.7 + - + +
125A PRO* 4.3 12.8 - - + -
141A TRP* 3.8 28.9 - - + +
143A LEU* 3.9 16.2 - - + -
156A PHE* 4.3 20.2 - - + -
227A PHE* 5.0 3.4 - - + -
229A TYR* 4.4 23.8 - - + +
346A PHE* 3.4 4.6 - - - -
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Residues in contact with THR 88 (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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84A ALA 2.6 23.0 + - - +
87A LEU* 1.3 74.4 - - - +
89A GLY* 1.3 62.6 + - - +
90A ARG* 3.3 25.6 + - - +
95A ASN* 3.4 13.2 + - + -
117A ILE* 4.0 5.4 - - + -
121A GLU* 3.2 44.4 - - + +
122A GLN 4.1 5.1 - - - +
123A LEU* 3.4 18.8 - - + -
346A PHE* 3.5 24.3 - - - -
363A ILE* 4.2 1.2 - - - +
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Residues in contact with GLY 89 (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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85A ALA 2.9 12.1 + - - -
88A THR* 1.3 76.5 - - - +
90A ARG* 1.3 57.9 + - - +
343A MET* 3.7 15.0 - - - -
346A PHE* 3.4 30.3 - - - +
363A ILE* 3.8 2.8 - - - +
364A ASP* 2.9 26.3 + - - -
365A GLY 2.9 8.5 + - - -
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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