Contacts of the strand formed by residues 75 - 83 (chain G) in PDB entry 4CDC
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 TYR 75 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70G ILE 3.6 0.9 - - - +
71G VAL* 3.4 3.6 - - - +
72G LEU 2.9 35.0 + - - +
73G ASN* 3.1 25.5 - - + -
74G ASP* 1.3 81.2 - - + +
76G LYS* 1.3 63.5 + - - +
77G TRP* 4.1 18.6 - + + +
102G VAL* 4.1 12.6 - - + -
103G HIS* 3.4 9.9 - - - +
104G ASP* 3.3 40.7 + - + +
105G VAL* 4.2 0.6 - - - +
109G ASN* 4.4 12.6 + - + +
314K PHE* 5.0 11.8 - - - -
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Residues in contact with LYS 76 (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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69G GLU* 4.1 6.5 + - - +
70G ILE 3.2 6.5 - - - +
71G VAL* 4.0 20.6 - - + +
75G TYR* 1.3 76.5 - - - +
77G TRP* 1.3 62.4 + - - +
101G TRP 3.6 2.4 - - - +
102G VAL* 3.3 4.9 - - - -
103G HIS* 2.8 46.6 + - + +
105G VAL* 4.1 29.8 - - + +
285H LYS* 3.8 16.2 + - - +
288H GLN* 2.8 31.2 + - - +
321H TYR* 3.3 30.2 + - - +
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Residues in contact with TRP 77 (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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17G PHE* 3.5 41.1 - + + -
19G VAL* 3.7 28.3 - - + -
40G VAL* 4.0 33.7 - - + -
42G VAL* 5.2 3.9 - - + +
68G PHE* 3.8 3.6 - - + +
69G GLU* 3.2 8.6 - - - +
70G ILE* 2.8 59.1 + - + +
72G LEU* 4.5 10.2 + - + +
75G TYR* 4.1 18.9 + + + +
76G LYS* 1.3 76.1 - - - +
78G PHE* 1.3 60.3 + - - +
101G TRP 3.7 4.5 - - - -
102G VAL* 3.3 30.1 - - + +
113G PHE* 3.7 23.1 - + + -
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Residues in contact with PHE 78 (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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63G ILE* 3.9 11.4 - - + -
67G GLY* 5.0 0.4 - - - -
68G PHE* 3.2 15.9 - - - +
69G GLU* 4.5 3.6 - - + -
77G TRP* 1.3 76.7 - - - +
79G ALA* 1.3 79.4 + - - +
80G PHE* 3.7 34.8 - + - -
100G GLY* 3.2 0.7 - - - -
101G TRP* 2.9 59.0 + + + +
113G PHE* 3.2 6.0 - - - -
270H TYR* 3.5 30.7 - + - -
281H LEU* 3.6 28.9 - - + -
285H LYS* 3.6 28.0 - - + -
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Residues in contact with ALA 79 (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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67G GLY* 3.2 21.0 - - - -
68G PHE* 3.3 17.1 + - + -
78G PHE* 1.3 89.2 - - - +
80G PHE* 1.3 60.4 + - - +
97G THR* 3.7 30.5 - - + -
98G MET 3.9 3.1 - - - +
100G GLY* 3.8 14.1 - - - -
101G TRP* 5.3 0.4 - - - -
113G PHE* 3.7 15.7 - - + -
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Residues in contact with PHE 80 (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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2G THR* 4.0 15.0 - - + -
66G GLN* 3.5 32.8 - - + +
67G GLY 4.6 0.4 - - - -
78G PHE* 3.7 27.4 - + - -
79G ALA* 1.3 74.1 - - - +
81G PHE* 1.3 61.3 + - - +
83G TYR* 5.2 0.4 - + + -
97G THR* 3.3 5.9 - - - -
98G MET* 2.7 47.6 + - + +
99G THR 5.3 2.1 + - - -
101G TRP* 4.9 6.5 - + - -
269H GLN 3.8 19.3 - - - -
270H TYR 3.4 18.8 - - - -
272H GLN* 3.3 31.6 - - - -
278H PHE* 5.7 2.0 - + - -
281H LEU* 3.9 11.4 - - + -
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Residues in contact with PHE 81 (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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2G THR* 4.9 0.3 + - - -
4G ALA* 4.3 9.3 - - + +
6G CYS* 3.6 40.8 - - + -
7G THR 5.0 1.3 - - - -
11G LEU* 4.0 24.2 - - + -
15G TRP* 4.2 17.3 - + - -
62G ILE* 4.0 16.8 - - + -
65G ASN 3.8 2.7 - - - -
66G GLN 2.7 31.0 + - - +
67G GLY* 3.4 27.3 - - - -
68G PHE* 4.1 16.6 - + - -
80G PHE* 1.3 75.4 - - - +
82G LYS* 1.3 65.6 + - - +
83G TYR* 3.5 15.9 - - - -
93G TYR 4.7 1.3 - - - +
94G CYS 4.1 15.0 - - - -
96G GLU 3.7 13.5 - - - +
97G THR* 4.2 0.9 - - + +
98G MET* 3.7 1.6 - - - +
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Residues in contact with LYS 82 (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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80G PHE 3.6 1.2 + - - -
81G PHE* 1.3 73.4 - - - +
83G TYR* 1.3 67.5 + - - +
84G LYS* 4.1 27.7 - - - +
92G THR* 3.6 5.9 - - - +
93G TYR* 2.9 44.5 + - + +
96G GLU* 2.9 61.1 + - + +
97G THR* 3.7 13.6 - - - +
98G MET* 3.8 17.0 - - - +
116G LYS* 6.0 0.2 - - - +
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Residues in contact with TYR 83 (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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2G THR* 3.7 30.2 - - + +
3G PRO* 3.6 37.2 - - + +
4G ALA* 4.8 4.3 - - + +
80G PHE* 5.2 1.1 - + + -
81G PHE 3.5 13.5 - - - +
82G LYS* 1.3 79.0 - - - +
84G LYS* 1.3 70.5 + - - +
90G VAL* 5.7 1.6 - - + -
91G THR 3.3 13.2 - - - +
92G THR* 4.4 8.7 - - - +
93G TYR* 4.8 0.9 - - - -
98G MET* 3.6 41.1 - - + +
272H GLN* 5.5 4.3 - - - +
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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