Contacts of the strand formed by residues 17 - 24 (chain T) in PDB entry 5IYB
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 17 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128S THR* 5.9 0.5 - - - -
129S GLN 6.0 0.2 + - - -
15T ASN 3.3 4.6 + - - -
16T THR* 1.3 76.2 - - - +
18T VAL* 1.3 68.8 + - - +
19T TRP* 5.3 0.7 - - - -
109T ILE 3.2 7.0 - - - -
111T VAL* 3.7 23.8 - - - -
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Residues in contact with VAL 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126S ILE* 4.0 17.0 - - + -
127S PHE 3.9 8.5 - - - +
128S THR* 3.9 26.0 - - + -
16T THR* 4.6 12.8 - - + -
17T GLY* 1.3 79.6 - - - +
19T TRP* 1.3 71.2 + - - +
95T VAL* 5.1 6.7 - - + -
107T GLU* 6.1 2.5 - - + -
108T GLY* 5.0 6.1 - - - -
109T ILE 3.0 16.3 + - - +
110T VAL* 3.6 20.6 - - + -
111T VAL* 3.0 24.0 + - - +
112T GLN 3.6 0.9 + - - -
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Residues in contact with TRP 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125S TYR 3.7 0.5 - - - +
126S ILE* 3.5 9.6 - - - +
127S PHE* 3.1 45.0 + - + +
135S PHE* 5.2 14.1 - + - -
17T GLY 5.3 0.7 - - - -
18T VAL* 1.3 87.7 - - - +
20T LEU* 1.3 60.2 + - - +
21T VAL* 4.2 11.4 + - + -
43T LEU* 5.0 12.1 - - + -
45T ILE* 4.8 17.3 - - + -
54T VAL* 4.7 26.2 - - + -
83T PHE* 5.9 4.3 - + - -
85T LEU* 5.5 6.3 - - + -
110T VAL* 4.8 1.1 - - - -
111T VAL* 3.8 13.8 - - + +
112T GLN* 3.5 37.9 - - + +
114T ALA* 6.4 0.7 - - + -
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Residues in contact with LEU 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S ILE* 4.6 7.6 - - + -
124S TYR* 4.4 23.1 - - + -
125S TYR 3.5 16.2 - - - +
126S ILE* 3.9 16.2 - - + -
140S VAL* 4.7 0.4 - - + -
143S TRP* 4.0 16.8 - - + -
19T TRP* 1.3 73.1 - - - +
21T VAL* 1.3 58.6 + - - +
22T LYS 5.4 0.2 - - - +
93T LEU* 3.6 29.6 - - + -
110T VAL* 4.0 11.2 - - + -
112T GLN 2.7 15.5 + - - +
113T ARG* 3.3 18.1 - - + +
114T ALA 2.7 32.7 + - - +
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Residues in contact with VAL 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123S SER 3.7 2.6 - - - +
124S TYR* 3.7 1.6 - - - -
125S TYR* 3.1 29.8 + - - -
127S PHE* 3.9 31.6 - - + -
19T TRP* 4.7 10.1 - - + -
20T LEU* 1.3 84.8 - - - +
22T LYS* 1.3 72.8 - - - +
23T VAL* 3.8 15.5 + - + +
83T PHE* 3.6 37.0 - - + -
114T ALA* 3.2 16.2 - - + +
116T CYS 4.1 5.2 - - - +
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Residues in contact with LYS 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B GLU* 5.2 6.2 + - - +
550B MET 4.8 9.9 + - - -
551B GLU* 5.0 3.6 - - - +
552B ASN 5.0 0.2 - - - +
555B GLU* 2.7 40.6 + - - -
122S THR* 4.0 28.2 - - + +
123S SER 3.5 4.7 - - - -
124S TYR* 3.5 25.1 - - + -
20T LEU* 4.3 0.4 - - - +
21T VAL* 1.3 70.9 - - - +
23T VAL* 1.3 59.6 + - - +
24T PRO* 4.7 0.2 - - - -
113T ARG* 6.1 0.2 - - - +
114T ALA 2.8 14.9 + - - +
115T GLU* 4.0 30.3 + - + +
116T CYS* 2.5 36.4 + - - +
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Residues in contact with VAL 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122S THR* 3.5 6.0 - - - -
123S SER* 2.9 39.9 + - - +
125S TYR* 3.5 39.5 - - + -
127S PHE* 5.5 1.8 - - + -
21T VAL* 3.9 17.5 - - + +
22T LYS* 1.3 80.3 - - - +
24T PRO* 1.3 76.6 - - + +
27T LEU* 4.3 16.6 - - + -
28T SER* 4.7 2.2 - - - +
31T TRP* 4.8 7.6 - - + -
83T PHE* 5.3 2.9 - - + -
116T CYS* 3.7 13.9 - - + -
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Residues in contact with PRO 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547B GLU* 6.1 7.0 - - + +
121S ASN 4.4 6.7 - - - +
122S THR* 4.9 1.3 - - + -
23T VAL* 1.3 92.2 - - + +
25T LYS* 1.3 64.7 + - - +
26T TYR* 3.4 37.9 - - + +
27T LEU* 3.3 16.7 + - + +
28T SER* 3.4 8.7 + - - -
116T CYS* 3.1 35.0 - - + +
118T PRO* 4.7 9.2 - - + -
124T TYR* 4.0 7.6 - - - +
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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