Contacts of the strand formed by residues 90 - 98 (chain A) in PDB entry 1CD8
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 GLY 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.5 10.1 - - - -
38A GLN 3.6 5.6 - - - -
39A PRO 4.2 6.7 - - - -
88A ASN 3.4 2.8 + - - -
89A GLU* 1.3 74.9 - - - +
91A TYR* 1.3 66.8 + - - -
92A TYR* 4.2 1.6 - - - -
108A VAL 3.7 0.2 - - - +
109A PRO* 3.6 2.9 - - - +
110A VAL* 2.8 33.8 + - - +
111A PHE* 3.7 13.7 - - - -
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Residues in contact with TYR 91 (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 PHE* 3.3 6.4 - - - -
38A GLN* 2.8 43.0 + - + +
39A PRO 4.4 0.2 - - - -
40A ARG* 3.7 44.6 + - - -
90A GLY* 1.3 74.9 - - - -
92A TYR* 1.3 60.4 + - - +
93A PHE* 4.2 1.6 - - - -
107A PHE* 3.6 57.2 - + + -
108A VAL 3.5 2.2 - - - -
109A PRO* 3.8 18.6 - - + -
111A PHE* 3.8 31.4 - + - -
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Residues in contact with TYR 92 (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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18A VAL* 6.0 0.4 - - + -
20A LEU* 3.7 21.3 - - + -
35A TRP* 4.0 8.1 - - + -
36A LEU 3.3 5.2 - - - +
37A PHE* 3.4 25.3 - + - -
49A LEU* 3.8 22.7 - - + -
68A PHE* 4.7 8.7 - + - -
79A LEU* 3.7 24.2 - - + -
81A LEU* 3.6 14.1 - - + +
88A ASN* 2.8 43.7 + - - +
90A GLY 4.0 2.5 - - - -
91A TYR* 1.3 77.7 - - - +
93A PHE* 1.3 61.6 + - - +
107A PHE* 4.7 0.2 - - - -
108A VAL* 2.9 38.1 + - + +
110A VAL* 3.6 32.1 - - + -
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Residues in contact with PHE 93 (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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5A VAL* 5.6 0.4 - - - -
35A TRP* 3.4 12.8 - - - -
36A LEU* 2.9 70.8 + - + +
37A PHE 4.4 0.2 - - - -
38A GLN* 4.0 20.6 - - + -
46A PRO* 3.7 25.1 - - + -
91A TYR 4.3 1.3 - - - -
92A TYR* 1.3 78.6 - - - +
94A CYS* 1.3 62.6 + - - +
104A PHE* 3.5 32.5 - + + -
105A SER* 3.6 16.4 - - - +
106A HIS 3.7 8.7 - - - +
107A PHE* 3.5 35.9 - + + -
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Residues in contact with CYS 94 (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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3A PHE* 3.8 7.9 - - + -
22A CYS* 2.0 51.1 - - + -
33A CYS* 3.6 13.2 - - - -
34A SER 3.2 4.5 - - - -
35A TRP* 3.2 30.1 - - - -
36A LEU* 4.7 0.2 - - - -
93A PHE* 1.3 77.9 - - - +
95A SER* 1.3 62.7 + - - +
104A PHE* 3.3 7.1 - - - +
105A SER* 2.8 38.0 + - - +
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Residues in contact with SER 95 (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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3A PHE* 4.0 3.6 - - - -
32A GLY 3.7 0.5 - - - +
33A CYS* 3.4 6.2 - - - -
34A SER* 2.9 38.7 + - - -
36A LEU* 3.6 23.1 - - - -
94A CYS* 1.3 76.0 - - - +
96A ALA* 1.3 59.9 + - - +
102A MET* 4.4 10.6 - - - +
103A TYR 2.8 18.4 + - - -
104A PHE* 3.4 16.2 - - - -
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Residues in contact with ALA 96 (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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3A PHE* 3.6 21.4 - - + -
24A VAL* 4.7 6.1 - - + -
26A LEU* 4.1 14.8 - - + -
29A PRO* 5.5 1.3 - - + -
31A SER* 3.8 5.4 - - - +
32A GLY 3.8 16.8 - - - +
33A CYS* 4.6 4.0 - - - -
95A SER* 1.3 76.4 - - - +
97A LEU* 1.3 64.7 + - - +
102A MET* 3.8 1.2 - - - -
103A TYR* 3.0 30.6 + - - +
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Residues in contact with LEU 97 (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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26A LEU* 4.5 1.9 - - - +
29A PRO* 3.4 4.7 - - - +
30A THR* 2.7 42.4 + - + -
31A SER* 2.8 28.3 + - - +
96A ALA* 1.3 76.7 - - - +
98A SER* 1.3 59.1 + - - +
100A SER* 4.3 14.8 - - - +
101A ILE 3.3 20.9 - - - +
102A MET* 3.6 31.4 - - + +
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Residues in contact with SER 98 (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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26A LEU* 3.2 20.2 - - - +
28A ASN* 2.8 27.0 + - - -
29A PRO* 3.2 10.3 - - - +
30A THR* 3.2 6.3 - - - +
97A LEU* 1.3 70.1 + - - +
99A ASN* 1.3 72.0 + - - +
100A SER 3.4 0.4 - - - -
101A ILE* 3.0 25.4 + - - +
103A TYR* 3.8 17.9 - - - -
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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