Contacts of the strand formed by residues 135 - 140 (chain H) in PDB entry 1C1V
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 LYS 135 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H GLY 4.1 2.9 - - - +
134H TYR* 1.3 76.1 - - - +
136H GLY* 1.3 62.5 + - - +
164H ASN* 4.7 3.8 - - + +
165H LEU 3.1 8.3 - - - +
166H PRO* 3.7 20.2 - - + -
190H TYR* 3.6 27.4 + - - +
192H LYS* 4.9 5.9 - - - +
207H MET* 3.4 6.6 - - - +
14L SER* 2.8 107.2 + - + +
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Residues in contact with GLY 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H TYR 4.0 0.4 + - - -
135H LYS* 1.3 76.1 - - - +
137H ARG* 1.3 60.5 + - - -
138H VAL* 5.0 0.2 - - - +
164H ASN* 3.2 6.7 - - - +
165H LEU 2.8 31.0 + - - -
205H PHE* 3.7 22.4 - - - -
206H VAL 3.5 11.7 - - - -
207H MET* 4.0 5.4 - - - -
14L LEU* 4.6 5.6 - - - -
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Residues in contact with ARG 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H MET* 4.1 11.4 + - - +
27H SER* 5.0 5.1 + - - -
136H GLY* 1.3 72.4 - - - -
138H VAL* 1.3 67.3 + - - +
139H THR* 4.2 10.8 - - + -
162H VAL* 3.3 28.1 - - + +
163H VAL 3.4 4.0 - - - +
164H ASN* 3.1 24.2 + - - +
204H PRO 3.6 1.2 - - - +
205H PHE* 3.2 5.5 - - - -
206H VAL* 2.9 47.4 + - + +
213H TRP* 3.3 27.7 - - - -
4L ARG* 3.8 7.1 - - - +
14L LEU* 2.7 84.8 + - + +
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Residues in contact with VAL 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ILE* 4.0 12.3 - - + +
136H GLY 5.0 0.2 - - - +
137H ARG* 1.3 78.5 - - - +
139H THR* 1.3 73.4 + - - +
162H VAL* 3.5 1.4 - - - -
163H VAL* 3.1 44.1 + - + +
165H LEU* 4.4 6.1 - - + -
196H ALA* 4.6 4.3 - - + -
200H ASP* 5.7 0.2 - - + -
204H PRO 3.5 11.0 - - - +
205H PHE* 3.6 23.3 - - + -
219H VAL* 3.4 34.1 - - + -
234H TYR* 3.7 19.5 - - + +
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Residues in contact with THR 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ILE* 4.4 6.5 - - - -
27H SER* 3.5 26.5 + - - +
29H TRP* 5.7 0.5 + - - -
30H GLN* 2.8 30.6 + - - +
137H ARG* 4.2 7.4 - - + -
138H VAL* 1.3 86.8 - - - +
140H GLY* 1.3 60.0 + - - +
160H LEU* 4.3 8.1 - - + -
161H GLN 3.1 17.3 - - - +
162H VAL* 3.9 21.1 - - + -
200H ASP* 4.2 7.3 - - - +
203H GLY* 4.7 4.7 - - - -
204H PRO* 4.0 14.8 + - - +
206H VAL* 6.4 1.1 - - + -
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Residues in contact with GLY 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ILE* 4.1 1.9 - - - +
30H GLN* 4.5 7.2 - - - -
139H THR* 1.3 78.8 - - - +
141H TRP* 1.3 59.1 + - - -
142H GLY 3.3 6.5 + - - -
160H LEU* 3.4 14.1 - - - +
161H GLN* 3.1 34.2 + - - +
199H GLY 5.3 0.2 - - - -
200H ASP* 3.2 17.0 + - - +
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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