Contacts of the strand formed by residues 153 - 158 (chain I) in PDB entry 5KZ5
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 GLN 153 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G ASN 4.5 2.6 + - - -
152G LYS* 3.4 36.4 - - - +
147I LYS* 4.7 0.2 - - - +
148I GLN* 3.0 35.3 + - + -
151I ASN* 3.6 25.4 + - + +
152I LYS* 1.4 80.2 - - - +
154I ILE* 1.3 67.5 + - - +
155I TRP* 5.1 1.6 - - + +
165I ARG* 3.7 24.7 + - - +
166I TYR 3.3 19.9 - - - +
167I ASP* 4.1 19.7 - - + +
168I TRP* 5.4 2.9 - - + -
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Residues in contact with ILE 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I ALA* 5.0 10.5 - - + +
103I LEU* 4.1 29.4 - - + -
145I ILE* 4.2 17.0 - - + -
146I ASN 3.5 8.3 - - - +
147I LYS* 4.0 21.1 - - + +
152I LYS 4.7 5.2 - - - +
153I GLN* 1.3 84.3 - - - +
155I TRP* 1.4 59.9 + - - +
166I TYR* 3.1 38.8 + - + +
168I TRP* 5.9 2.0 - - - +
173I TRP* 5.4 6.5 - - + -
182I LEU* 3.8 42.4 - - + -
91S ARG* 5.2 0.4 - - - +
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Residues in contact with TRP 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152G LYS* 6.1 4.7 - - - +
144I VAL* 3.6 7.2 - - + +
145I ILE* 3.7 0.3 - - - -
146I ASN* 3.0 65.2 + - - +
148I GLN* 5.0 8.2 - - + +
153I GLN* 4.2 2.2 - - + -
154I ILE* 1.4 73.5 - - - +
156I LEU* 1.4 58.6 + - - +
157I SER* 4.1 20.2 - - - -
163I PRO* 3.3 39.7 + - + +
164I LYS 3.5 14.4 - - - -
165I ARG* 3.8 28.3 - - + +
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Residues in contact with LEU 156 (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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143I TYR* 4.0 13.0 - - + -
144I VAL 3.6 2.2 - - - +
145I ILE* 3.7 41.7 - - + -
154I ILE 4.0 1.4 + - - -
155I TRP* 1.4 72.8 - - - +
157I SER* 1.3 70.5 + - - +
158I SER* 3.7 8.3 + - - +
162I GLY 3.9 0.2 - - - +
163I PRO* 3.2 4.8 - - - +
164I LYS* 3.0 54.7 + - + +
166I TYR* 3.9 30.1 - - + +
182I LEU* 4.6 5.6 - - + +
185I LEU* 4.2 9.4 - - + -
186I LEU* 4.6 11.9 - - + -
189I GLU* 5.2 2.7 - - - +
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Residues in contact with SER 157 (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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159D PRO* 4.4 12.0 + - - +
142I THR 5.1 2.5 + - - -
143I TYR* 3.2 28.6 - - - +
144I VAL* 2.8 33.7 + - - +
155I TRP* 3.9 20.8 + - - -
156I LEU* 1.3 69.9 - - - +
158I SER* 1.4 59.8 + - - +
159I PRO 4.1 0.2 - - - -
162I GLY 4.0 2.7 - - - -
163I PRO* 4.1 13.5 - - - +
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Residues in contact with SER 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D PRO 3.2 7.5 - - - +
143I TYR* 3.5 17.4 - - - -
156I LEU* 3.7 6.8 + - - +
157I SER* 1.4 73.4 + - - +
159I PRO* 1.3 58.2 - - - +
160I SER* 3.0 21.9 + - - -
161I SER* 3.5 16.7 + - - -
162I GLY 2.8 40.3 + - - +
164I LYS* 3.7 14.0 + - - -
189I GLU* 3.8 4.0 + - - -
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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