Contacts of the strand formed by residues 108 - 114 (chain I) in PDB entry 5A0Q
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 PRO 108 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7I VAL* 4.3 17.9 - - + -
8I TYR 4.8 1.3 - - - +
9I LYS 4.9 5.2 - - - +
10I ASP 4.8 3.6 - - - +
11I GLY* 3.8 22.4 - - - +
12I ILE* 3.5 19.1 - - + -
102I GLY 3.6 7.9 - - - +
103I VAL* 3.7 9.4 - - + -
107I GLY* 1.3 84.8 - - - +
109I HIS* 1.3 70.3 + - - +
121I LYS* 3.6 10.3 - - - -
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Residues in contact with HIS 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I VAL* 5.0 0.2 - - - -
12I ILE* 3.5 3.8 - - - +
75I ARG* 6.4 0.2 - - + -
76I VAL* 3.3 33.1 - - + +
77I VAL* 4.0 16.9 - - + +
101I GLY* 3.4 2.1 - - - -
102I GLY 3.0 31.3 + - - +
106I THR* 3.3 34.3 + - - -
107I GLY 3.3 9.1 + - - -
108I PRO* 1.3 84.9 + - - +
110I LEU* 1.3 61.2 + - - +
111I TYR* 3.5 28.3 - + + -
121I LYS* 3.8 22.7 - - + +
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Residues in contact with LEU 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I GLY* 3.5 31.2 - - - +
6I VAL* 3.6 16.4 - - - +
7I VAL* 3.4 15.2 - - + +
12I ILE* 3.8 8.1 - - + -
14I LEU* 3.7 19.5 - - + -
99I VAL* 3.4 33.4 - - + -
100I LEU 3.3 11.2 - - - +
101I GLY* 4.2 0.4 - - - -
109I HIS* 1.3 75.9 - - - +
111I TYR* 1.3 58.9 + - - +
112I SER 4.0 0.5 + - - -
120I ASP 4.0 0.3 - - - +
121I LYS* 3.2 21.4 - - - +
122I LEU 3.3 23.0 + - - +
123I PRO 3.9 1.1 - - - +
125I VAL* 4.1 10.8 - - + +
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Residues in contact with TYR 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I VAL* 4.8 0.2 - - + -
77I VAL* 3.6 23.2 - - - +
80I ASN* 2.5 48.0 - - + +
99I VAL* 3.7 2.6 - - - -
100I LEU 2.9 32.0 + - - -
109I HIS* 3.5 26.0 - + + -
110I LEU* 1.3 76.7 - - - +
112I SER* 1.4 67.5 + - - +
113I ILE* 3.4 8.0 - - + +
119I THR* 3.7 20.9 - - - -
120I ASP* 3.5 8.3 - - - +
121I LYS* 3.1 33.4 - - + +
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Residues in contact with SER 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I LEU 3.9 4.0 - - - -
99I VAL* 4.5 1.6 - - - +
110I LEU 4.0 1.8 + - - -
111I TYR* 1.4 70.9 - - - +
113I ILE* 1.3 59.7 + - - +
114I TYR* 3.6 28.0 + - - -
118I SER 3.5 1.0 - - - +
119I THR* 3.5 1.6 - - - -
120I ASP* 3.1 34.9 + - - +
125I VAL* 3.8 34.6 - - - +
126I THR 4.2 5.8 + - - -
127I MET* 3.3 18.6 - - - +
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Residues in contact with ILE 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80I ASN* 3.6 17.3 - - - +
83I LEU* 3.5 43.7 - - + +
84I LYS* 4.9 0.2 - - - -
87I LEU* 3.5 22.0 - - + +
97I ALA* 3.4 4.5 - - - +
98I LEU* 2.9 38.0 + - + +
100I LEU* 4.3 4.9 - - + -
111I TYR 3.4 12.3 - - - +
112I SER* 1.3 79.8 + - - +
114I TYR* 1.3 64.0 + - - +
117I GLY* 4.7 2.2 - - - -
118I SER 3.0 18.8 - - - +
119I THR* 3.5 18.4 - - + -
127I MET* 3.5 1.9 - - - +
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Residues in contact with TYR 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H THR* 5.6 4.7 - - + -
25H TYR* 5.5 3.1 - - - -
27H ALA* 3.7 27.8 - - + +
300H KNM 4.0 36.1 - - + -
87I LEU* 3.9 2.1 - - - +
97I ALA* 4.2 1.8 - - + -
112I SER* 3.6 30.1 + - - -
113I ILE* 1.3 78.1 - - - +
115I PRO* 1.3 72.2 - - + +
116I HIS 3.1 4.3 - - - +
117I GLY* 2.9 21.5 + - - -
118I SER* 3.2 22.6 + - - +
120I ASP* 5.1 9.9 - - + -
126I THR 4.5 7.9 + - - -
127I MET* 4.6 15.9 - - + -
135I MET* 5.0 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